Call-Back: All the way back to "Outbreak", which is where Don picked up the mutagen in the first place. Bishop bringing Stockman back in a new cyborg body is also a reference to "Insane in the Membrane".
Chekhov's Gun: The tunnel to April's apartment: introduced in "The Trouble with Augie".
Continuity Nod: this episode features April's basement apartment, which hadn't been seen or referenced since "The King," three seasons earlier. It even had the appropriate pieces of furniture in it, like Kirby's drawing desk.
Downer Ending: Donatello is left a mutated, mindless monster that must be kept in a cell.
Resist the Beast: Donny's transformation into mindless beast is obviously painful, yet he's able to resist it for long enough to beg April and Casey to 'stay away from' him as he runs from the room, only to turn into a monster and start attacking them.
The Smart Guy: Leatherhead takes up Donnie's role as this in the team.
Unwanted Revival: Bishop retrieves Stockman's brain and attaches it to a new cyborg body, needing him to work on a cure for the outbreak. Stockman is absolutely mortified that he wasn't left to rest in peace.