When the Soviets come back to the USA with more men, and bigger guns, they will leave themselves open to resistance movements
in their own territories.
And the next Freedom Fighters
game will put us in charge of the resistance from Europe, Asia, Africa or maybe even the Glorious Mother Russia
The unfinished Liberty Island level was supposed to give closure for what happened to Troy
General Bulba remaining The Un Fought
and the generally rather rushed feel of the ending suggest that there was supposed to be at least one proper mission after retaking Governor's Island that ended up cut for time. We also only have the unsubstantiated word of The Mole
that Troy was actually killed at all, though it does seem quite likely that he is in fact dead.
The Soviets were never able to fully occupy North America and were still trying to eliminate all resistence on the continent but got sidetracked by Chris and the other movements behind the front lines.
I don't recall any part of Canada being taken by the Soviets, and pressure from both US cities and from a Back from the Brink
push from Canada and/or whatever parts of the US the Soviets couldn't get to (The Rockies? Hawaii?) would help explain a mass withdrawl less than a year after cold-cocking ths US.