Spoiler!
Flynn turns into the monster and is now forever traveling through alternate timelines of Echo.
Spoiler
"Sam" used Flynn's desire to learn the truth to mutilate Flynn into a body that he can use to ride the "ebb and flow" of Echo. Flynn desperately wanted to know what happened to Sidney and he was ultimately denied that possibility when he traveled back in time to the incident and his eyes dissolved. You'll see more of the Sam/Flynn monster in other routes but it doesn't seem to be evil. In fact it seems to play the part of a vigilante at times. "We make the justice we are given"
OMGGGG now I get it!!!! now I understand why he said that (We make the justice we are given). And It's so true that this route is so cruel and like a tragedy with all the Sidney's dead and the crazyness of Flynn :( He deserved a better ending where he could forget about sidney and where he would live in peace with carl