The last season, he went against the goverment. Including the president, for the greater good ofc.
Finaly at the end the president realized her mistakes, but by then everyone was aware of Jacks betrayal, without knowing why. Only a select few knew the presidents choices, good or bad.
At the end, ppl got the order to take out Jack (kill him), ppl ordered by presidents office. Then the president called it off, and decided to come clean. She let Jack go and said he's still considered a traitor and that he needs to escape.
I'm guessing she didn't come fully clean, hence Jack still being a traitor + all the other ppl he killed/hurt high up, in the world goverment controlling team, etc.
Hope it helps!
