Ok so you know how you can either kill or capture javier for agent ross to take alot of people kill javier but i....well I capture him almost all of the time,its because javier felt innocent its like javier turned into a monster because of dutch brainwashing the gang infect when micah says Arthur's lying you can see javier hold his gun in the air it seems like he dosent wanna kill them he still thinks of them as family
So that's why I spare javier