Apparently the parasites hitched a ride on the green energy crystals Rick picked up while Morty was killing Fart: imageand tweet.
That shit got dark as hell with Beth at the end there. Guess she really is her father's daughter. . .
I do suspect that the Jerry-switch will come back into play soon enough. IIRC, it was only after the swap that he started speaking with his hip new urban flair, and of course the new Jerry seems to have some bi leanings I didn't pick up on before then, either. . .
edit: There's also mounting evidence that the Rick who we originally saw interacting with the C-137 family (the original family from "Pilot" to "Rick Potion No. 9") was not from their dimension in the first place. Specifically, aside from the fact that he can obviously dimension-hop at will, he has made a few cultural references that seemed genuine that no one else got or knew about, like his trying to figure out the name of the Tom Cruise move he thought he saw (Cuisine) and calling Tiny Richard Tiny Roger instead.
Which would now mean that living in the Current Dimension (designation unknown) is Unknown Dimension Rick, C137 Morty (sole un-Cronenberged human inhabitant of that dimension still living), Current Dimension Summer and Beth, and Swapped Dimension Jerry.
This family's getting complicated as fuck pretty quickly, and given Harmon's established love for callbacks and long cons in his comedies (e.g., Beetlejuice in Community), I can't help but think some or all of that stuff will crop up sooner or later.