He was a soldier in the OCU military. He stopped obeying military orders after one of his missions killed his wife. As a result he was imprisoned for insubordination. He is promised freedom by Semaun Forsyth, commander of Taal Base, if he fights once again for OCU.
In Emma storyline, if the player choose the below course directly to inside of mountain, team will meet him as the enemy that must be defeated after Lukav saves Alisa and scientists. He is also the one who beats up the Purple Haze. He will fight Kazuki and team along side Semaun.
If the player chose the uphill course, team will meet him inside the mountain guarding transport plane. After defeating him in a battle, Kazuki talks to him and it changes his way of life. In the last battle of Taal Base, Jose becomes ally and fight alongside the team against Semaun Forsyth and his giant wanzer, Monsters.
In Alisa storyline, Jose will always be the enemy no matter which course the player choose. And player will meet him at the last battle of Taal Base, fighting along side Semaun.