Once again, John Noble stole an episode of Fringe despite being largely sidelined. He only had a handful of scenes as Walter, and he was mostly stuck at HQ as Walternate. But there's no doubt who the most magnetic character on this show is. Both Walters revealed something about themselves and made some tough choices, in an episode that contrasted the love of shapeshifters with the love of doppelgangers.
So it's pretty clear that Walternate was still kind of a bastard in this timeline, even if he was perhaps not as awful as the version we know. Everybody assumed he was behind this latest rash of shapeshifters, and he even admits towards the end of this episode that he's sort of a polarizing figure in the transdimensional community. (Although this Walternate didn't kill and dismember his version of Broyles.)
But now Walternate is facing a bigger, more manipulative bastard than he is — and he's being completely outflanked. Walternate tried to be sneaky, autopsying the dead shapeshifter himself and exposing Brandon's treachery. But he's totally missed the fact that alt-Broyles is a shapeshifter, and he gets totally played by David Robert Jones, who allows himself to get captured so he can get his hard drive back from Brandon's office. Walternate gives in to Jones' terrorism and blackmail, reasoning that they can keep tabs on Jones and gain more intel that way. But Jones evades the Fringe team's surveillance by tossing out dollar bills with cloned trackers on them, and then runs rings around our gang.
And meanwhile, Walternate decides to help Peter, a version of his son from a whole different timeline, but quickly finds that he can't make any use of the blueprints to the Machine. Leading to a heart-to-heart with his wife, Elizabeth, who's a lot more proactive and perspicacious in this timeline. (A side note: I keep remembering what a wasted opportunity it was last season, when they randomly gave Walternate a mysterious girlfriend played by Joan Chen, who gave him pep talks — instead of giving him more scenes with Elizabeth. What was up with that?)
So Elizabeth goes to see Walter, as seen in the clip above, and convinces him to help Peter — by telling him that she forgave him a long time ago. In this universe, Walter never got the white tulip, and thus never felt like he was forgiven for his crime of crossing universes. John Noble once again produces an amazing performance, as a Walter who's been in a much darker place than any version we've seen previously. It's kind of neat that this time around, we get to see him getting forgiveness and love from the woman he wronged most of all when he first crossed universes — the double of his wife who killed herself.
So both Walters learn to do whatever is necessary for Peter, because he's the double of their dead son, and he's the closest they'll ever come to seeing their own sons grow up and make a life for themselves. Helping Peter get back to loved ones is the least they can do, since they'll never get to have an adult Peter in their own lives.
Meanwhile, while the Walters are learning to love the doppelganger of Peter, David Robert Jones makes a startling declaration of love — he loves his Shapeshifters, like a father. All 40-odd of them, they're his precious babies. This is somewhat undercut by the fact that he kills one of them as he says this, and he sacrifices other shapeshifters to advance his plans throughout the episode.
What does it mean to love shapeshifters? Does Jones envy their ability to change their form, since he's stuck in a fairly hideous shape? Does he have a mad scientist's love for his creations? Does he he love them because they sacrifice for him?
And meanwhile, Peter's finally decided to take part in the fight, because he has knowledge of Jones that nobody else has. And he's made himself a target, taunting Jones with his knowledge and announcing loudly that he's the good guys' main asset in the fight against Jones. How long before Fake Broyles sends someone to rub Peter out? At least he's got Walter's help, and Walter's back in the house where he belongs.
(Oh, and "our" Lincoln realizes that Fauxlivia and alt-Lincoln are just friends, even though Fauxlivia finally broke up with boring old Frank. Guess Lincoln's got his work cut out for him with Olivia.)
In any case, Jones zips between universes with their help, getting the rare mineral he needs to blow a giant hole in the multiverse — and his ally turns out to be Nina Sharp, who's totally straight-up evil in this timeline. She raised Olivia and her sister after their mom died, but now she has no compunction about using Olivia as a pawn in her schemes, experimenting on her to get her ready for "Phase Two" of the Jones-Sharp master plan. It's actually quite sinister. Because I guess whatever love Jones has for his shapeshifters and the Walters have for their not-quite-son, Nina doesn't have it for her adopted daughter.