Lincoln Lee — feeling unwanted, unloved, unneeded — heads over to the other side (remember? That whole other universe?) to, I forget, work a little harder on tracking David Robert Jones? Anyway, the other side’s Fringe team catches a case of a serial killer who’s targeting criminals. He might not have been discovered for some time, but the other universe has been stabilizing and healing, thanks to the bridge between worlds, which is allowing some previously amberized neighborhoods (where the killer is stashing bodies) to open back up — and which means that Fringe agents there — as opposed to Earth-1, where they operate as secretively as possible — are seen as heroes.
It’s our Lincoln who figures out the killer’s a shapeshifter, and they manage to track him down with the evil Col. Broyles keeping evil Nina Sharp (is there a name for the evil Nina? Sharpie?) in the loop. Lincoln Lee — who’s having an identity crisis thanks to the reblossoming romance between Olivia and Peter, and now the fact that Lincoln Bee is a kickass, uber-confident super-agent — also determines that the shapeshifting killer (Canaan) is not such a bad guy, but someone who turned to David Robert Jones (who has abandoned him) in a time of vulnerability that naturally mirrors how Lincoln Lee is feeling.
Evil Nina almost has Canaan taken out by sniper, who is then taken down by Fauxlivia, quite the sharpshooter herself, remember, but not before Lincoln Bee is shot. Then Canaan shapeshifts into the sniper so that Fringe can infiltrate the Fort Lee facility where Nina is being all nefarious, and she’s arrested. No one appears to find out yet that Col. Broyles is evil. But Fringe’s joy at discovering a treasure trove of information on Jones’ network is tempered when Lincoln Bee dies of his injuries. Lincoln Lee takes Canaan over to our side, where the Bishops can give him a home and a starring role as a research project, and then Lincoln Lee decides he’s going to stick around for a while in the other universe. Fauxlivia looks like she appreciates it, which is all he’s asking for.