It was Saix. He was the one who approached Vexen and the one who had been sabotaging Xehanort’s 13 Darknesses with his plans behind the scenes. He had been a traitor since he joined the first Organization. The only thing that caused him to go astray from his own plans was his jealousy towards Axel. He believed Lea forgot about him and X because he became friends with Roxas and Xion. Even in his jealousy, he still attempts to atone because he cares about Lea and the memory of X.
The new purpose Saix came upon was his plan to undermine the 13 Darknesses by sabotaging their efforts from the inside by implanting those who would not fall in line with Xehanort’s plans, and also from the outside by helping the Lights regain Roxas.
While it is not explained fully, this was essentially what was going on. You see it when Saix first “greets†Vexen into their ranks by asking him if he is sure this was the choice he wanted to make, and that the second chance at humanity is a gift one should treasure. Then again when Saix nonchalantly sits down with Axel to eat ice cream. He was reaffirming his devotion to finding X and showing that his goals did not align with Xehanort’s. It’s why the scene plays out the way it does. Axel’s trying to diss Saix and Saix is just trying to have an ice cream break. The secret reports make it more clear that Isa has never fallen in line with the Organization.