Spoiler Warning - this has lots of story spoilers and some things from KHIII in regards to Union-X!
Theory One: The killer and the darkness is Luxu, the replacement is Ephemer. I think Luxu killed Strelitzia because he saw her as being the weakest of the five dandelion leaders and felt that she was expendable. He then gave her rule book to Ephemer (he saw the figure while exploring the sewers/cloak tower and uttered "you!?!"), which would imply that the dandelions or at least Ephemer had previously acquainted themselves with Luxu and/or the Master of Masters. Luxu as "The Darkness" knew Brain had infiltrated his master's carefully constructed program and took matters into his own hands to eliminate/expose the imposter (which is why he later traps Maleficent in a data version of Enchanted Dominion, and why she and Pete are present at the foreteller reunion in the KH3 Epilogue). In Kingdom Hearts III secret reports supposedly penned by Luxu himself indicate that he was well aware of the goings on with the new union leaders in the other Daybreak Town and he couldn't know all of this without actually being there himself or having an accomplice (or being Phoenix-Jean Grey levels of clairvoyant). I believe that while Ephemer is the replacement or stand-in for Strelitzia, he is neither the killer or the imposter as he was chosen by the MoM/Luxu (the timing of which is irrelevant in this case due to the arrival of the virus).
Questions: I thought the Master of Masters was a kind, and fun-loving guy why would he want his apprentice(s) to go around killing little girls and instigating paranoia and suspicion among friends? Well the MoM turned all five Foretellers against one another, making each believe that there was a "traitor" and allowed a bloody keyblade war to erupt which saw the deaths of hundreds of children from Daybreak Town, so he is already an established passive-aggressive sadistic narcissist who may also have some megalomaniacal tendencies unless we're reading too deeply into his name/title and possibly the ending of the Yozora secret movie movie. Also with Luxu we don't know much about KHuX Luxu, however Xigbar/Braig Luxu is a conniving, ruthless, capable fighter willing to do whatever it takes to get the job done. He has shown he has the ability to act and can adapt to new environments, meaning it wouldn't be out of place for him to kill one of Ava or the MoM's chosen to plant a more capable agent.
But what about the hooded figure? Either they haven't been shown yet (will most likely be resolved in a KH Back Cover II: Union-X) or is "the darkness", but not the killer (see Theory Three).
Theory Two: The killer and the darkness is Luxu, the replacement is Ventus, this theory plays off of my first theory with the idea that Luxu is the killer while Vanitas/Ventus is the replacement. Basically all of the above but switch out Ephemer with Ventus and Brain is still the virus.
Theory Three: Luxu is the killer, Strelitzia is the darkness. Basically this theory carries parts of my first two theories, meaning that any two of the boys are replacements (either Ephemer or Ventus, but not both) Brain is the virus disrupting the Master's and by extension, Luxu's plans and Strelitzia or more accurately her nobody is the darkness that has been preventing future!Maleficent from causing chaos (or a paradox). This is kind of weird but bear with me, Luxu still killed Strelitzia (seeing her as the weakest and most expendable, etc) BUT Strelitzia continues to serve Luxu and The Master of Masters in nobody form as "the darkness". Alternately the darkness is not Strelitzia's nobody, but her heartless (similar to Ansem Seeker of Darkness).
Theory Four: Luxu is Brain, Ephemer is the Virus and Strelitzia is the Darkness. This theory assumes that Luxu is indeed fulfilling his role as an observer of events and has infiltrated the group of dandelions, meanwhile Ephemer is the imposter (note: that this is assuming Luxu/Brain killed Strelitzia and replaced her while Ephemer usurped her spot). We can see a dream/vision sequence wherein Ephemer is exploring the sewers/clocktower and is greeted by a mysterious figure (darkness?) and utters a startled "you!?!" Assuming this took place after Strelitzia's death, it can be surmised that Strelitzia had already become a heartless/nobody and undertaken the "darkness" mantle. It may be possible that the rule book she gave to Ephemer was once Ava's, and that the copy she originally owned when she was killed is now in possession of Brain/Luxu. Strelitzia gave Ava's rule book to Ephemer in secret, told him about the new unions and where to meet and warned him of a killer (she was struck from behind so she likely did not see her killer's face). This works in the sense that Strelitzia's nobody/heartless is actively working against Luxu/MoM possibly under Ava's guidance (the darkness mentions a master to Maleficent, but does not outright say "Master of Masters" meaning it could be any of the five foretellers or even the MoM and/or Luxu).
Questions: Why is Ephemer the virus, when Brain openly referred to himself as such? Because Ephemer reached the unchained realm (somehow) and probably gained glimpses into the future and awakened worlds, this knowledge would most likely present a threat to the Master of Masters' carefully concocted plans (i.e. why he didn't give Luxu a Book of Prophecies, etc.) How can Luxu be Brain when the former didn't receive a book of prophecies from the MoM, and the latter was shown reading a copy? Well assuming that Brain is in fact Luxu, then we know by KHIII that he has had many forms and has existed throughout various generations in time, which means that a version of him in KHuX exists for Xigbar to send his heart backwards in time, so in this instance the whole paradox issue of the book is more or less a moot point because future!present Brain (Luxu) has lived a long time and has seen it all, so it's really just a matter of him sticking to the script so to speak.
Theory Four: Vanitas is the killer, the darkness and the replacement. This theory claims that Vanitas (the dark half of Ventus) is in full-control of Ventus during the events of KHuX, killed Strelitzia, took her rule book and insinuated himself among the dandelion leaders under Luxu's advisement. In this scenario Vanitas is an agent of Luxu, likely communicating via the gazing eye in each other's keyblades (which how Luxu/Xigbar became aware of the virus situation among the dandelions in the KH3 secret reports).
Questions: Why would Vanitas follow someone like Luxu? Why wouldn't he? Ever since his initial appearance Vanitas has taken orders from someone higher up on the food chain; in both Birth by Sleep and KH3 it was Master Xehanort and in Union-X it is Luxu, the connection being that they both bear the recusant's sigil and wield the No Name keyblade. Also Vanitas is not necessarily a nice guy by any means and I doubt it would take much convicing to make him go about sewing chaos.
Theory Five: The Darkness is all four foretellers. This theory basically assumes that the remaining four foretellers (due to Master Ava's prolonged absence) are still active even after the keyblade war and in the other Daybreak Town world. This would mean that each time a shadowy silhouette is shown, it is potentially a different foreteller and they are all acting in accord with Luxu and the MoM's plans.
Questions: But last we saw the Foretellers hated each other, mistrusted one another and were attacking each other. Honestly I have no idea how they became buddy-buddy again after that, but it seemingly does happen (probably explained in Back Cover II: Union-x). In Kingdom Hearts III aside from emotions of surprise and confusion, and questioning Xigbar's motives the Foretellers did not seem at all hostile towards one another. One possibility is that the foretellers we thought we saw during the original Chi keyblade war and Back Cover (more likely the former) were illusions or more accurately data prepared and activated by the Master of Masters in order to ensure that a Keyblade War does happen as prophesized, but without losing his five valued apprentices. This theory of course excludes Ava, whom out of the five is the only one to question Luxu and actually seem to mistrust him.
Theory Six: The Hooded figure is Ava, but is not "Darkness". This theory suggests that the hooded figure on the cover of the Union-x artwork (login screen) is actually Master Ava in a black coat and NOT Strelitzia (nobody/heartless) or Luxu. This also implies that the hooded figure is likely working with someone (possibly Brain -the virus) offscreen, and is supplying them with the power and know-how to counteract Luxu and MoM's plans. Master Ava CANNOT be darkness in this scenario as Darkness even states outright to Maleficent that a virus has wormed its way into their "Master's" program, and at this point we're assuming Ava has gone rogue in an attempt to revert/undo the Keyblade War or at least derail the Master of Masters & Luxu's plans. Ava plants Brain among the Dandelion leaders as a monkey-wrench to clog the Master's gears. Alternately Ephemer is the "virus" being aided in secret by Master Ava, and Brain is Luxu.
Questions: The hooded figure hasn't even appeared yet in-game, and why would Ava work against the Master of Masters? Assuming that "Darkness" isn't Master Ava in disguise then it's possible that the hooded person on the cover is her. Why? Because she is directly connected to Strelitzia, she is holding a bleeding heart flower symbolizing the tragic death of a young girl (Strelitzia is a young girl who recently died) and actually chose Strelitzia to be a union leader. Also in Kingdom Hearts III Xigbar expresses no shock that Ava is not present for the reunion, which prompts Gula to ask if he had deliberatley excluded her from coming and he basically just says that he flat-out told her he was just obeying orders from the MoM. This lines up with the confrontation between Luxu and Ava from when just before the keyblade war broke out, she questions and accuses him of being the traitor and attacks him. Why would Ava just attack Luxu for no reason? Ava didn't just blindly attack Luxu, she suspected him of being the traitor, when in fact Ava herself is the traitor to the overall cause of the Master of Masters and the Foretellers (we're ignoring the whole "traitor bears the recusant's sigil" because it could just be a mindscrew from the MoM and/or pertain to something entirely different). Other reasons include; being shadowy, witholding information, being passive-aggressive about preventing the keyblade war (and preventing the deaths of children), etc. and basically Luxu's intentions were evil and he was doing them in behalf of his Master, therefore Ava is working against the MoM because she believes his actions are evil, or at the very least not beneficial for mankind.
Theory Seven: Luxu is Brain, Ventus/Vanitas is the Darkness and Ephemer is the Virus.
This theory borrows from number six, Master Ava is working offscreen in alliance with Ephemer who had reached the Unchained Realm and is using him as a "Virus" against Luxu and The Master of Masters. Luxu is Brain, while he refers to himself as a virus, from a gameplay and story point of view this is most likely a red herring to throw people off the scent of the "real virus" (Ephemer). Vanitas is the darkness that appeared before Ephemer in the sewers/clocktower (alternately Ava is the mysterious figure Ephemer saw and used that opportunity to make him her agent), and trapped Maleficent in the data Enchanted Dominion. The "my master" that Darkness refers to is none other than Luxu (Brain) who is working to bring the current worldline back into sync with the Master of Masters' vision. Ephemer is the virus because he became unchained, and has a former foreteller (unbeknowst to Luxu) aiding him and his knowledge of future events could potentially unravel the MoM's carefully concocted plans.
Questions: But why would Luxu be among the Dandelion leaders when he's supposedly gone missing/supposed ot be handing down his keyblade? Assuming that the dandelions aren't aware of Luxu's physical appearance, and given his previous (or more accurately "future" acting capabilities) it is fair to assume that Luxu can act and adapt to any situation in order to blend in with his surroundings (he posed as a "fool desirous of the keyblade" for several years under Xehanort).
Theory Eight: Ephemer is the virus, the killer and the darkness. This theory assumes that Ephemer fell to darkness, or was at least partially consumed by it and that the Nightmare Chirithy was actually his and not the player's. Ephemer killed Strelitzia in order to seize an opportunity to become a Union Leader and make the necessary changes to sustaining the world. This theory also assumes that neither Ventus or Brain are imposters, but Brain could still possibly be Luxu. Eventually it comes to light that Ephemer had killed Strelitzia or that he was the last one seen with her, Lauriam exacts revenge and kills Ephemer in return (Ephemer in Final World in KH3), but his heart full of darkness lives on as a powerful heartless in the remnants of the keyblade war as the "Dark Inferno" (if we are to believe that the Dark Inferno IS Ephemer's heartless). The union descended into chaos as Skuld attacks Lauriam in return, he is wounded and becomes a nobody. Elrena attacks Skuld, but Ventus aids her and she too becomes a nobody. Skuld and Ventus go up against Brain (who is Luxu) and lose, Skuld somehow reaches Radiant Garden albeit amnesiac (see Subject-X secret reports) and Ventus winds up in the keyblade graveyard (see events of Birth By Sleep). Brain/Luxu's master virus comes to fruition as Daybreak Town is transmogrified into Scala ad Caelum, where he will begin the long procession of handing down his keyblade from apprentice to apprentice.
Questions: But Ephemer is a nice guy, why would he hurt a fellow dandelion much less kill them? Because he was corrupted by darkness? This whole theory supported only by the basis that The Nightmare Chirithy is Ephemer's (and not x-player's) and that sometime between meeting player and becoming Union-x leader, became corrupted by darkness. (Note: A lot of the original nightmare chirithy dialogue and content was cut from the mobile release, as well as the majority of the keyblade war - so the assumption that the Nightmare is Ephemer's could work in this instance.) Basically the possibility of power can lead people to doing some pretty terrible things (see what KH1 Riku, BBS Terra and Xehanort all did).
Summation: In closing I believe the closest theory to the truth is a combination of Theories 1, 4, 6 and 7. IF Brain is Luxu then I think he truly is a "virus" but not the virus mentioned in the secret reports, because the virus he mentions is a union leader not on the MoM's approved list. I believe that Ava is aiding the virus (Brain if not Luxu, otherwise Ephemer) offscreen in some capacity in combating Luxu/The MoM. I really do think that Brain is Luxu as well as the darkness. His words and actions of late have shown to alarm Skuld and Ventus and he seems to be acting in coordination with some sort of grand plan. Aside from your x-player character, Ephemer is more or less the hero of Union-x which would make sense from this viewpoint that he is actually the "virus" mentioned in the KH3 Secret Reports.
Is Master Ava the hooded figure on the cover? There is a good possibility of it either being Ava or Strelitzia, probably more likely the latter seeing as how she is holding a bleeding heart and standing parallel to her brother who is holding a dandelion (tragedy symbolism vs hope/fulfillment symbolism). IF Brain is the Virus but not Luxu, then this is where theory 6 comes in and Vanitas is the mole, whereas Luxu is "the darkness" and the killer also working from the shadows to combat the virus (Brain - only if he is NOT Luxu, otherwise Ephemer).
The person Ephemer saw and expressed surprised at could be the darkness, but it seems more likely that it was Master Ava. I believe the whole darkness persona is your atypical shadowy silhouette that is used as a red herring to keep people guessing. In this case it is to make all of use presume that Master Ava is missing alongside her fellow foretellers, however the events of KH3 reveal that she is still missing and before that she was confronting Luxu so it seems safe to say that she is acting in one way or another to keep her dandelions safe. If that person he were in fact darkness or even Luxu or the killer (if Brain or Luxu is the killer and/or each other) it could be expected that they would probably use the opportunity to attack him, and the sentiment expressed by Ephemer seemed to indicate that it was someone he knew but not any of the current Union leaders and most likely not Luxu. If the Nameless Star (from KH3) is in fact Strelitzia, then it most likely also rules her out of being both the hooded figure and the silhouette making it even more susceptible that the silhouette and the hooded figure was/is Master Ava. This does not contradict the Ephemer/silhouette meeting or the darkness/maleficent meeting or the silhouette killing Strelitzia in that all three can be different individuals, but for gameplay and story reasons are obscured to throw us off and keep us guessing. My best bet is that "darkness" (silhouette who met with Maleficent) is Luxu AND Brain, the Silhouette who met with Ephemer is Master Ava, and the shadowy warehouse killer is again Luxu/Brain.
I don't believe Lauriam or Elrena were involved in any capacity in Strelitzia's murder or any of the time travel/darkness shenanigans. The silhouette has been shown to match Lauriam's height and shape, however as I mentioned before this is likely a red-herring meant to make it seem obvious that Lauriam is guilty. Brain is also an obvious red herring, but not in the way that we are expecting. Again like I mention before, assuming Brain is Luxu then he is the virus but not in the same manor mentioned in the reports - he is a virus acting on behalf of the MoM in order to rewrite the program back to its original process. I could throw in that while the killer is most likely Luxu/Brain but that Darkness is Vanitas/Ventus, again I feel that it is too much of an obvious go to (like in KH3 Vanitas calls himself darkness and then you have this character saying the same, it's too convenient) I think the Killer & Darkness are all one in the same, but the sewer/clock tower silhouette is someone else entirely (Master Ava), and Brain AND Ephemer are both viruses but for different purposes.
Sorry for the looooooong stream of consciousness posting. Whenever I get an idea I have to put it to pen and paper or type it out otherwise I will forget it
TL;DR - Lauriam is innocent, Ava is the hooded girl on front/sewer silhouette, Ephemer & Brain are both viruses, Brain is really Luxu and the killer/darkness, and Daybreak Town is transforming into Scala ad Caelum to uncertain means.
Theory One: The killer and the darkness is Luxu, the replacement is Ephemer. I think Luxu killed Strelitzia because he saw her as being the weakest of the five dandelion leaders and felt that she was expendable. He then gave her rule book to Ephemer (he saw the figure while exploring the sewers/cloak tower and uttered "you!?!"), which would imply that the dandelions or at least Ephemer had previously acquainted themselves with Luxu and/or the Master of Masters. Luxu as "The Darkness" knew Brain had infiltrated his master's carefully constructed program and took matters into his own hands to eliminate/expose the imposter (which is why he later traps Maleficent in a data version of Enchanted Dominion, and why she and Pete are present at the foreteller reunion in the KH3 Epilogue). In Kingdom Hearts III secret reports supposedly penned by Luxu himself indicate that he was well aware of the goings on with the new union leaders in the other Daybreak Town and he couldn't know all of this without actually being there himself or having an accomplice (or being Phoenix-Jean Grey levels of clairvoyant). I believe that while Ephemer is the replacement or stand-in for Strelitzia, he is neither the killer or the imposter as he was chosen by the MoM/Luxu (the timing of which is irrelevant in this case due to the arrival of the virus).
Questions: I thought the Master of Masters was a kind, and fun-loving guy why would he want his apprentice(s) to go around killing little girls and instigating paranoia and suspicion among friends? Well the MoM turned all five Foretellers against one another, making each believe that there was a "traitor" and allowed a bloody keyblade war to erupt which saw the deaths of hundreds of children from Daybreak Town, so he is already an established passive-aggressive sadistic narcissist who may also have some megalomaniacal tendencies unless we're reading too deeply into his name/title and possibly the ending of the Yozora secret movie movie. Also with Luxu we don't know much about KHuX Luxu, however Xigbar/Braig Luxu is a conniving, ruthless, capable fighter willing to do whatever it takes to get the job done. He has shown he has the ability to act and can adapt to new environments, meaning it wouldn't be out of place for him to kill one of Ava or the MoM's chosen to plant a more capable agent.
But what about the hooded figure? Either they haven't been shown yet (will most likely be resolved in a KH Back Cover II: Union-X) or is "the darkness", but not the killer (see Theory Three).
Theory Two: The killer and the darkness is Luxu, the replacement is Ventus, this theory plays off of my first theory with the idea that Luxu is the killer while Vanitas/Ventus is the replacement. Basically all of the above but switch out Ephemer with Ventus and Brain is still the virus.
Theory Three: Luxu is the killer, Strelitzia is the darkness. Basically this theory carries parts of my first two theories, meaning that any two of the boys are replacements (either Ephemer or Ventus, but not both) Brain is the virus disrupting the Master's and by extension, Luxu's plans and Strelitzia or more accurately her nobody is the darkness that has been preventing future!Maleficent from causing chaos (or a paradox). This is kind of weird but bear with me, Luxu still killed Strelitzia (seeing her as the weakest and most expendable, etc) BUT Strelitzia continues to serve Luxu and The Master of Masters in nobody form as "the darkness". Alternately the darkness is not Strelitzia's nobody, but her heartless (similar to Ansem Seeker of Darkness).
Theory Four: Luxu is Brain, Ephemer is the Virus and Strelitzia is the Darkness. This theory assumes that Luxu is indeed fulfilling his role as an observer of events and has infiltrated the group of dandelions, meanwhile Ephemer is the imposter (note: that this is assuming Luxu/Brain killed Strelitzia and replaced her while Ephemer usurped her spot). We can see a dream/vision sequence wherein Ephemer is exploring the sewers/clocktower and is greeted by a mysterious figure (darkness?) and utters a startled "you!?!" Assuming this took place after Strelitzia's death, it can be surmised that Strelitzia had already become a heartless/nobody and undertaken the "darkness" mantle. It may be possible that the rule book she gave to Ephemer was once Ava's, and that the copy she originally owned when she was killed is now in possession of Brain/Luxu. Strelitzia gave Ava's rule book to Ephemer in secret, told him about the new unions and where to meet and warned him of a killer (she was struck from behind so she likely did not see her killer's face). This works in the sense that Strelitzia's nobody/heartless is actively working against Luxu/MoM possibly under Ava's guidance (the darkness mentions a master to Maleficent, but does not outright say "Master of Masters" meaning it could be any of the five foretellers or even the MoM and/or Luxu).
Questions: Why is Ephemer the virus, when Brain openly referred to himself as such? Because Ephemer reached the unchained realm (somehow) and probably gained glimpses into the future and awakened worlds, this knowledge would most likely present a threat to the Master of Masters' carefully concocted plans (i.e. why he didn't give Luxu a Book of Prophecies, etc.) How can Luxu be Brain when the former didn't receive a book of prophecies from the MoM, and the latter was shown reading a copy? Well assuming that Brain is in fact Luxu, then we know by KHIII that he has had many forms and has existed throughout various generations in time, which means that a version of him in KHuX exists for Xigbar to send his heart backwards in time, so in this instance the whole paradox issue of the book is more or less a moot point because future!present Brain (Luxu) has lived a long time and has seen it all, so it's really just a matter of him sticking to the script so to speak.
Theory Four: Vanitas is the killer, the darkness and the replacement. This theory claims that Vanitas (the dark half of Ventus) is in full-control of Ventus during the events of KHuX, killed Strelitzia, took her rule book and insinuated himself among the dandelion leaders under Luxu's advisement. In this scenario Vanitas is an agent of Luxu, likely communicating via the gazing eye in each other's keyblades (which how Luxu/Xigbar became aware of the virus situation among the dandelions in the KH3 secret reports).
Questions: Why would Vanitas follow someone like Luxu? Why wouldn't he? Ever since his initial appearance Vanitas has taken orders from someone higher up on the food chain; in both Birth by Sleep and KH3 it was Master Xehanort and in Union-X it is Luxu, the connection being that they both bear the recusant's sigil and wield the No Name keyblade. Also Vanitas is not necessarily a nice guy by any means and I doubt it would take much convicing to make him go about sewing chaos.
Theory Five: The Darkness is all four foretellers. This theory basically assumes that the remaining four foretellers (due to Master Ava's prolonged absence) are still active even after the keyblade war and in the other Daybreak Town world. This would mean that each time a shadowy silhouette is shown, it is potentially a different foreteller and they are all acting in accord with Luxu and the MoM's plans.
Questions: But last we saw the Foretellers hated each other, mistrusted one another and were attacking each other. Honestly I have no idea how they became buddy-buddy again after that, but it seemingly does happen (probably explained in Back Cover II: Union-x). In Kingdom Hearts III aside from emotions of surprise and confusion, and questioning Xigbar's motives the Foretellers did not seem at all hostile towards one another. One possibility is that the foretellers we thought we saw during the original Chi keyblade war and Back Cover (more likely the former) were illusions or more accurately data prepared and activated by the Master of Masters in order to ensure that a Keyblade War does happen as prophesized, but without losing his five valued apprentices. This theory of course excludes Ava, whom out of the five is the only one to question Luxu and actually seem to mistrust him.
Theory Six: The Hooded figure is Ava, but is not "Darkness". This theory suggests that the hooded figure on the cover of the Union-x artwork (login screen) is actually Master Ava in a black coat and NOT Strelitzia (nobody/heartless) or Luxu. This also implies that the hooded figure is likely working with someone (possibly Brain -the virus) offscreen, and is supplying them with the power and know-how to counteract Luxu and MoM's plans. Master Ava CANNOT be darkness in this scenario as Darkness even states outright to Maleficent that a virus has wormed its way into their "Master's" program, and at this point we're assuming Ava has gone rogue in an attempt to revert/undo the Keyblade War or at least derail the Master of Masters & Luxu's plans. Ava plants Brain among the Dandelion leaders as a monkey-wrench to clog the Master's gears. Alternately Ephemer is the "virus" being aided in secret by Master Ava, and Brain is Luxu.
Questions: The hooded figure hasn't even appeared yet in-game, and why would Ava work against the Master of Masters? Assuming that "Darkness" isn't Master Ava in disguise then it's possible that the hooded person on the cover is her. Why? Because she is directly connected to Strelitzia, she is holding a bleeding heart flower symbolizing the tragic death of a young girl (Strelitzia is a young girl who recently died) and actually chose Strelitzia to be a union leader. Also in Kingdom Hearts III Xigbar expresses no shock that Ava is not present for the reunion, which prompts Gula to ask if he had deliberatley excluded her from coming and he basically just says that he flat-out told her he was just obeying orders from the MoM. This lines up with the confrontation between Luxu and Ava from when just before the keyblade war broke out, she questions and accuses him of being the traitor and attacks him. Why would Ava just attack Luxu for no reason? Ava didn't just blindly attack Luxu, she suspected him of being the traitor, when in fact Ava herself is the traitor to the overall cause of the Master of Masters and the Foretellers (we're ignoring the whole "traitor bears the recusant's sigil" because it could just be a mindscrew from the MoM and/or pertain to something entirely different). Other reasons include; being shadowy, witholding information, being passive-aggressive about preventing the keyblade war (and preventing the deaths of children), etc. and basically Luxu's intentions were evil and he was doing them in behalf of his Master, therefore Ava is working against the MoM because she believes his actions are evil, or at the very least not beneficial for mankind.
Theory Seven: Luxu is Brain, Ventus/Vanitas is the Darkness and Ephemer is the Virus.
This theory borrows from number six, Master Ava is working offscreen in alliance with Ephemer who had reached the Unchained Realm and is using him as a "Virus" against Luxu and The Master of Masters. Luxu is Brain, while he refers to himself as a virus, from a gameplay and story point of view this is most likely a red herring to throw people off the scent of the "real virus" (Ephemer). Vanitas is the darkness that appeared before Ephemer in the sewers/clocktower (alternately Ava is the mysterious figure Ephemer saw and used that opportunity to make him her agent), and trapped Maleficent in the data Enchanted Dominion. The "my master" that Darkness refers to is none other than Luxu (Brain) who is working to bring the current worldline back into sync with the Master of Masters' vision. Ephemer is the virus because he became unchained, and has a former foreteller (unbeknowst to Luxu) aiding him and his knowledge of future events could potentially unravel the MoM's carefully concocted plans.
Questions: But why would Luxu be among the Dandelion leaders when he's supposedly gone missing/supposed ot be handing down his keyblade? Assuming that the dandelions aren't aware of Luxu's physical appearance, and given his previous (or more accurately "future" acting capabilities) it is fair to assume that Luxu can act and adapt to any situation in order to blend in with his surroundings (he posed as a "fool desirous of the keyblade" for several years under Xehanort).
Theory Eight: Ephemer is the virus, the killer and the darkness. This theory assumes that Ephemer fell to darkness, or was at least partially consumed by it and that the Nightmare Chirithy was actually his and not the player's. Ephemer killed Strelitzia in order to seize an opportunity to become a Union Leader and make the necessary changes to sustaining the world. This theory also assumes that neither Ventus or Brain are imposters, but Brain could still possibly be Luxu. Eventually it comes to light that Ephemer had killed Strelitzia or that he was the last one seen with her, Lauriam exacts revenge and kills Ephemer in return (Ephemer in Final World in KH3), but his heart full of darkness lives on as a powerful heartless in the remnants of the keyblade war as the "Dark Inferno" (if we are to believe that the Dark Inferno IS Ephemer's heartless). The union descended into chaos as Skuld attacks Lauriam in return, he is wounded and becomes a nobody. Elrena attacks Skuld, but Ventus aids her and she too becomes a nobody. Skuld and Ventus go up against Brain (who is Luxu) and lose, Skuld somehow reaches Radiant Garden albeit amnesiac (see Subject-X secret reports) and Ventus winds up in the keyblade graveyard (see events of Birth By Sleep). Brain/Luxu's master virus comes to fruition as Daybreak Town is transmogrified into Scala ad Caelum, where he will begin the long procession of handing down his keyblade from apprentice to apprentice.
Questions: But Ephemer is a nice guy, why would he hurt a fellow dandelion much less kill them? Because he was corrupted by darkness? This whole theory supported only by the basis that The Nightmare Chirithy is Ephemer's (and not x-player's) and that sometime between meeting player and becoming Union-x leader, became corrupted by darkness. (Note: A lot of the original nightmare chirithy dialogue and content was cut from the mobile release, as well as the majority of the keyblade war - so the assumption that the Nightmare is Ephemer's could work in this instance.) Basically the possibility of power can lead people to doing some pretty terrible things (see what KH1 Riku, BBS Terra and Xehanort all did).
Summation: In closing I believe the closest theory to the truth is a combination of Theories 1, 4, 6 and 7. IF Brain is Luxu then I think he truly is a "virus" but not the virus mentioned in the secret reports, because the virus he mentions is a union leader not on the MoM's approved list. I believe that Ava is aiding the virus (Brain if not Luxu, otherwise Ephemer) offscreen in some capacity in combating Luxu/The MoM. I really do think that Brain is Luxu as well as the darkness. His words and actions of late have shown to alarm Skuld and Ventus and he seems to be acting in coordination with some sort of grand plan. Aside from your x-player character, Ephemer is more or less the hero of Union-x which would make sense from this viewpoint that he is actually the "virus" mentioned in the KH3 Secret Reports.
Is Master Ava the hooded figure on the cover? There is a good possibility of it either being Ava or Strelitzia, probably more likely the latter seeing as how she is holding a bleeding heart and standing parallel to her brother who is holding a dandelion (tragedy symbolism vs hope/fulfillment symbolism). IF Brain is the Virus but not Luxu, then this is where theory 6 comes in and Vanitas is the mole, whereas Luxu is "the darkness" and the killer also working from the shadows to combat the virus (Brain - only if he is NOT Luxu, otherwise Ephemer).
The person Ephemer saw and expressed surprised at could be the darkness, but it seems more likely that it was Master Ava. I believe the whole darkness persona is your atypical shadowy silhouette that is used as a red herring to keep people guessing. In this case it is to make all of use presume that Master Ava is missing alongside her fellow foretellers, however the events of KH3 reveal that she is still missing and before that she was confronting Luxu so it seems safe to say that she is acting in one way or another to keep her dandelions safe. If that person he were in fact darkness or even Luxu or the killer (if Brain or Luxu is the killer and/or each other) it could be expected that they would probably use the opportunity to attack him, and the sentiment expressed by Ephemer seemed to indicate that it was someone he knew but not any of the current Union leaders and most likely not Luxu. If the Nameless Star (from KH3) is in fact Strelitzia, then it most likely also rules her out of being both the hooded figure and the silhouette making it even more susceptible that the silhouette and the hooded figure was/is Master Ava. This does not contradict the Ephemer/silhouette meeting or the darkness/maleficent meeting or the silhouette killing Strelitzia in that all three can be different individuals, but for gameplay and story reasons are obscured to throw us off and keep us guessing. My best bet is that "darkness" (silhouette who met with Maleficent) is Luxu AND Brain, the Silhouette who met with Ephemer is Master Ava, and the shadowy warehouse killer is again Luxu/Brain.
I don't believe Lauriam or Elrena were involved in any capacity in Strelitzia's murder or any of the time travel/darkness shenanigans. The silhouette has been shown to match Lauriam's height and shape, however as I mentioned before this is likely a red-herring meant to make it seem obvious that Lauriam is guilty. Brain is also an obvious red herring, but not in the way that we are expecting. Again like I mention before, assuming Brain is Luxu then he is the virus but not in the same manor mentioned in the reports - he is a virus acting on behalf of the MoM in order to rewrite the program back to its original process. I could throw in that while the killer is most likely Luxu/Brain but that Darkness is Vanitas/Ventus, again I feel that it is too much of an obvious go to (like in KH3 Vanitas calls himself darkness and then you have this character saying the same, it's too convenient) I think the Killer & Darkness are all one in the same, but the sewer/clock tower silhouette is someone else entirely (Master Ava), and Brain AND Ephemer are both viruses but for different purposes.
Sorry for the looooooong stream of consciousness posting. Whenever I get an idea I have to put it to pen and paper or type it out otherwise I will forget it
TL;DR - Lauriam is innocent, Ava is the hooded girl on front/sewer silhouette, Ephemer & Brain are both viruses, Brain is really Luxu and the killer/darkness, and Daybreak Town is transforming into Scala ad Caelum to uncertain means.
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