Colonel Broyles pinpoints the maintenance closet where Lincoln is hidden. He loads up a syringe and heads out. But he's derailed by the arrival of Peter and Walternate, who orders Lincoln released. Walternate explains about the human shapeshifters and Agent Murphy. Broyles says that Agents Lee and Dunham are following up on Murphy's last phone call right now.
Bolivia and Agent Lee arrive at David Robert Jones' warehouse, where he stands calmly by a tank holding a shapeshifter. He speaks of feeling a parent's love for his creations - all 47 of them. Suddenly, gas pours into the tank, killing the shapeshifter. He wants them to understand how ruthless he can be. Now take him to their leader.
At Harvard, Olivia privately gives Astrid a blood sample to research. She confesses that she helped Peter and Lincoln cross over and now she has to tell Broyles, because they're not back.
Bolivia and Agent Lee deliver Jones to Col. Broyles. They can't ID him, and he knew they were coming and cleared out the warehouse. Meanwhile, Lincoln tells Peter that he wants to join the investigation, but Peter again rants that he needs to get home. Then he sees Jones.
Col. Broyles questions Jones, who demands that they bring him a hard drive hidden in Dr. Fayette's office. They have 12 minutes. Walternate sends Bolivia and Lee. Jones predicts that they'll let him go, then asks for a cup of tea.
Peter tells Walternate that the man is David Robert Jones, a scientist with a background in biotechnology and genetic weaponry - who crossed over from the other universe. He asks to talk to him. Col. Broyles objects, but Walternate says OK.
Peter notes Jones' facial scars and mentions the molecular disintegration he suffered after transporting out of the German prison. He seems to have healed himself, perhaps with some sort of DNA graft? Rattled, Jones insists that he's never met Peter. No, but Peter's met him. He explains he closed the portal Jones opened to this universe, and cut him right in half. Jones says, you've run out of time. In a hospital ER, one of his minions triggers a device that kills ten people.
Meanwhile, Broyles tells Olivia that he knows about Peter and Lincoln's field trip. He fills her in on Jones, who broke out of a Frankfurt prison three years ago.
When Jones threatens a worse attack if he's not released within 14 minutes, Walternate gives in. Agent Lee tells the team he put an internal tracker in Jones' tea. Lincoln joins the surveillance detail.
After being released, Jones retrieves a thermos and a stack of cash from a trash can and starts giving away $100 bills. The icons on the Fringe tracking devices multiply rapidly. Jones put trackers on the money! Lincoln wonders how he knew what signal to use? Jones drinks from the thermos, then gets into a limo. It drives right past Col. Broyles, who merely watches it go.
Walternate tells Elizabeth he can't see how the Machine could return Peter to his timeline. He mentions Walter's refusal to help and laments that he can't help Peter himself. Elizabeth says maybe she can.
The information copied from Jones' hard drive includes geological data from government satellites. Peter figures out that he's searching for a mineral called amphylicite, found mostly under large limestone deposits. When processed a certain way, it can become a power source. Where Peter's from, William Bell used a tiny amount to create a battery, and Jones stole the battery. Even that little bit could blow a hole in the universe.
They determine that Jones is targeting the Mohonk Quarry. But as Fringe agents secure the location, Peter realizes they're guarding the quarry in the wrong universe.
Walter gets a visitor: Elizabeth Bishop. He says he's sorry; he had no right to try to save her Peter. God has punished him for it ever since. He asked for a sign of forgiveness, a white tulip, but got nothing. Well, Elizabeth forgives him. And if she can, God can. There's something of both their sons in this Peter. He deserves to return to his people.
Lincoln and Peter cross back to This Side. Elsewhere, Jones comes through a portal opened by his shapeshifters. At the quarry, his minions load rocks into a truck. The Fringe team barrels in, and Jones' people start shooting. Olivia radios that she's going after the truck carrying Jones, headed toward another portal. Peter warns it will close after Jones goes through, and kill her! She slams on the brakes. Half the SUV's front end disappears, but Olivia's OK.
Walternate addresses the team: both Olivias, both Broyleses, both Lincolns, and Peter. They know who their enemy is, but what's he planning? Lincoln laments that Jones holds all the cards. Not all, says Peter: You have me. Somewhere, they stopped him before, and they can stop him again. Together.
But first, Peter needs sleep. Olivia thanks him for saving her life.
Later, Walter visits Peter. Thanks to Elizabeth, he's ready to help. Walter thought he was an expert on loss, but maybe that's why Peter's here, because he still has things to learn. Peter says he was very surprised that the other Walter was not the man he thought he was. But he's not at all surprised to learn that Walter is. And, yes, that's a good thing.
Elsewhere, Jones types a message: "Phase One complete. Where do we stand on phase two?" A reply is typed by the gloved hands of Nina Sharp: "In due time. We're working on her. She'll be ready soon."