The episode begins with Broyles looking over some security footage. He sees their Olivia and two Lincolns going down a hall. A few minutes later, Olivia comes back with only one Lincoln. Looking at the expression on his face, I’m guessing that he knows the hallway does not lead to the real containment center. He checks the blueprints and finds the closet where our Lincoln is being held, before going to prepare a mysterious yellow liquid in a big scary needle.

He makes his way through headquarters to take care of it, but Walternate interrupts him. He asks to see agent Lee at once. Once they’re in private, Walternate warns Broyles about the shape shifters, and that he still doesn’t know who sent them and what their purpose is. Broyles assures Walternate that Olivia and Lincoln are following up on a phone trace from last episode’s suspect.

Lincoln and Olivia arrive at the scene. It’s an abandoned old building, of course. As they approach, a door opens. They draw their weapons and proceed. Our villain is opening some gas canisters as they enter and order him to freeze. He has a female shape shifter in some kind of tube. They watch in horror as she dies within the tube. He then asks them to take him to their leader.

Back on our side, Olivia enters the lab, where Walter is busily working on cooking with chemicals. Olivia has come to see Astrid. She needs a blood sample checked (probably Buddy’s). When Astrid asks what’s going on, Olivia admits that Peter and Lincoln have gone to the other side. Now Olivia has to go tell Broyles.

On the other side, erstwhile, Olivia and Lincoln return with their prisoner. Broyles is waiting for them. They don’t know who he is. He tells them to take David Robert Jones to interrogation. As they do so, Peter and our Lincoln are reunited. Peter informs Lincoln that it’s time to go home, but Walternate will keep him updated. Lincoln protests, but Peter doesn’t listen… until he spots the suspect.

The investigation commences with Jones and Broyles together in a room. Walternate is watching from behind the glass. He tells Broyles that there isn’t much time if they want to avoid deaths. He asks for something from fake Brandon’s office. There are only twelve minutes to retrieve it. Walternate sends Olivia and their Lincoln to fetch. Jones next says he expects they will end up letting him go, and asks for a cup of tea.

Peter and our Lincoln approach Walternate, who is displeased to see they haven’t gone home yet. Their attitude changes when Peter tells them who the suspect is, and what he can do. Walternate and Broyles permit Peter to talk to him. Jones is startled that Peter knows he is from the other universe, but he seems not to remember Peter.

Just then Broyles and Walternate receive a call from a friend of Jones. The woman is setting up a gas canister in a hospital that is designed to kill everyone in the hallway. It apparently causes their skin to fall apart in a bloody mess. (This hails back to the disgustingness of season one.)

On our side, Olivia approaches Broyles, who apparently knows everything already. He has been updated by the other Broyles already. They are going to help with the Jones situation.

On the other side, we find out there will be another attack in fourteen minutes unless Jones is released. Walternate sees no choice but to let him go. Our Lincoln is appalled, but there’s no choice. They hope to monitor him with an internal tracker, which their Lincoln has put in Jones’ tea. Our Lincoln asks to help with the investigation, and the other side accepts.

Once released, Jones asks for his hard drive, which he has been using to get into the satellites. He then walks out a free man.

We next go a park, where Jones is waiting to get lost in the lunch crowd. Olivia is sitting with our Lincoln. He asks if she and their Lincoln are close. She laughs at the idea, saying he has been her shoulder to cry on after she broke up with someone. But their conversation is cut off because Jones is on the move. He’s removing a canister from a paper bag, along with some money. He starts handing the money out for free, and so a crowd surrounds him.

Back at HQ, Jones’ tracking signal begins multiplying. He’s put trackers on the money, as he has somehow figured out what signal they were using. In the confusion, Jones disappears. (But I did spot an Observer in the crowd.)

Jones gets into a car in an alley. Broyles spots him driving away but does nothing. He gives the order that everybody should return to Fringe Division.

In some restaurant, Walternate is sitting with his wife at dinner. He is writhing in guilt after making the call to let Jones go. Elizabeth guesses he is also upset after looking at the machine’s blueprints. He cannot help Peter, and he feels bad about it. He looks oddly Walter-like as he confesses his regret. But then Elizabeth wonders if perhaps she can help Peter.

Back at headquarters, other Astrid is telling Broyles that Jones was using the satellites for geothermal imaging. He is looking for something underground.

Our Lincoln approaches Olivia. He says that if Jones pinpointed the tracker’s wavelength that quickly, then someone must have given it to him. Astrid then announces that Peter knows where Jones is going. Peter thinks he was looking for a mineral that can be used to make a battery with enough power to blow a hole in the universe. They think he is heading for a certain quarry on the Hudson River.

Broyles goes there with his Lincoln and Olivia to secure the quarry. Meanwhile, the other Lincoln, Peter, and Astrid monitor from HQ. Peter warns them of an access road that Jones could use to flank them, but they don’t see it. Peter then realizes that Jones is not going to the quarry in that universe. Jones has traveled to our universe, where our favorite shape shifter is waiting for him.

On our side, Walter is visited by Elizabeth. She tells him that she’s not his Elizabeth, and she has come about Peter.

Our Broyles welcomes Peter and Lincoln. Peter tries to take the blame, but it doesn’t work.

At the lab, Walter serves Elizabeth tea. He apologizes for taking her Peter. He says he deserves his punishment. He never received a sign of forgiveness, but Elizabeth gives him hers. She begs him to help Peter. Walter confesses that he is afraid, but Elizabeth reminds him that Peter is, too.

At the quarry, our Fringe team finally catches up to Jones. Jones’ people open fire as Jones climbs into the truck carrying the cargo. Olivia chases after Jones. Peter calls for her to stop, but she chases Jones through the portal as it closes. She survives, but the front of her car is gone.

Next we see Walternate addressing a table of parties from both sides. They will work together, but they have to figure out what he’s going to do with the mineral. Peter promises them that they’ll have his help, too.

Olivia later asks him all about Jones. She wants to start right away, but Peter wants to sleep first. She also thanks him for stopping her from getting killed at the quarry.

Once Peter is home, Walter comes to his door. Peter asks if he’s all right, and Walter asks to come in. He was walked over by himself. He’s changed his mind. He will help Peter get home.

Meanwhile, Jones is communicating with someone, asking when “Phase Two” will commence. The person at the other end… Nina Sharp.