Neo

hes not back just a program written from strans of his memory or something like that

I play the game and he is now an non player character who can only be interacted with after level 25.

Missions granted include a lot of fetch quests and he discusses about what happened to him and where he has been while negotiating with the machines to create a peaceful coexistence for both. His advanced form appears after you reach level 30 where he transforms into a new version showing his rebirth and grants missions outside the matrix in the real world to overthrow the president who is really a machine.