On a rainy day on the Other Side, Captain Lincoln Lee is buried. Bolivia tells her murdered partner's parents that she'll bring those responsible to justice.
At Fringe HQ, Bolivia offers the other Nina Sharp a one-time-only deal: a reduced sentence for revealing David Robert Jones' mole in the Department of Defense. Nina refuses, then says that things may seem bad now, but it's going to get much worse.
On This Side, the Fringe team investigates after three men in different locations die simultaneously by being suddenly, violently, flung around. Their injuries are consistent with a plane crash, though none was in a plane. Walter has a theory that checks out: A chartered plane crashed on the Other Side at the same time, with three fatalities.
Bolivia shows Colonel Broyles a list of 108 people who would've known about the prisoner transport. Jones has been a step ahead all along, and she thinks that someone inside tipped off Nina Sharp and got her partner killed. Broyles says he'll cut through the red tape for her, but he needs her on this plane case.
Bolivia and Lincoln meet Walter at the Bridge. He'll be consulting on this investigation. Walter says he and William Bell never thought an event in one universe would cause a reaction in the other. Bolivia mentions what Nina said about things getting worse. Walter says if Jones caused this, he's conceived of something he and Belly never did.
Walter conducts an experiment involving tuning forks, a plane-crash victim from Bolivia's side, and the hand of a victim from his world. Each universe vibrates at its own specific frequency - Bolivia's at G, Walter's at C. But both bodies are on G. Somehow, the doppelgangers were linked. They listen to the recording of the pilot in mid-crash, and Walter says the aircraft was destabilized by whatever merged the frequencies - probably some kind of device.
A bespectacled minion tells Jones that the experiment with the plane went well. Does he have a preference for the next one? Surprise me, says Jones.
An unexpected visitor is waiting for Colonel Broyles at home. Jones gives him a case containing vials and hypodermic needles, saying his son Christopher is responding extraordinarily well to treatment. Just a few months ago, he was in constant pain, blind, and dying. Broyles knows that someday he'll have to account for his role in this . . . collaboration. But, says Jones knowingly, you can't lose your boy.
On This Side, Jones' minion leaves a briefcase in a cab. A woman gets in. On the Other Side, her doppelganger shops at a pet store. The device activates, plunging the cab off a bridge. The pet shop patron flies across the store and coughs up water.
The two Astrids meet again on the Other Side, to coordinate their teams' investigations. Our Astrid delights Farnsworth with a gift - coffee, that rarest of beverages. Peter finds the briefcase in the wrecked cab. Inside is a device powered by amphilicite.
When Walter complains about his accommodations, Bolivia invites him to stay with her. Privately, Walter tells Colonel Broyles that Jones couldn't do any of this without the right conditions - which Walter created by crossing over years ago. Broyles asks if he'd make the same choice again? A few months ago, Walter would've said no. But now that he's gotten to know Peter, he's not sure he'd do anything differently.
Farnsworth informs Bolivia that she ran that list of names Bolivia gave Broyles - twice - but found nothing.
Broyles meets Jones, who orders him to place a small device on the Machine's control panel, silencing his protests by reminding him about Christopher. At home, Broyles gives Christopher his meds as his son chatters about his great day.
Late at night, Walter finds Bolivia awake, tipsy from drinking whiskey left by her ex, Frank. She's looking for a mole in Fringe Division. She can't face Lincoln's parents until she knows something, and she thought the whiskey would give her courage, but it's just made her feel sick. Walter makes eggs and invokes Sherlock Holmes, whom Bolivia's never heard of. He says no evidence is evidence in and of itself, and suggests Colonel Broyles. She scoffs. He admonishes that, in the case of a mole, no one should be above suspicion.
Bolivia confronts Nina, bluffing that the mole, Broyles, is in custody and revealed all. Nina scoffs that he's only a pawn. Jones is still coming for her. Perhaps, says Bolivia . . . unless you're just another pawn.
As Bolivia and Lincoln discuss what Nina said, Farnsworth reports that no one has seen Colonel Broyles today, and his subcutaneous tracker was disabled two hours ago.
The Colonel gets Jones' device past the Bridge checkpoint. Farnsworth tracks him through his Show Me Card. Bolivia and Lincoln rush past the checkpoint and find the Colonel with This Side's Broyles. He's turned himself in. Colonel Broyles tells Bolivia that he's sorry.
As Walter departs, he tells Bolivia not to judge Colonel Broyles; no one knows how far they'll go to save loved ones. Lincoln's not going back until they find whoever killed Bolivia's partner - and his. He tells her it might not feel like it now, but it does get better.As Nina watches in disbelief, Colonel Broyles is locked in a cell.
Peter and Olivia rush into the Harvard lab. Walter soberly says that the two incidents were a test: Jones wanted to find a frequency that could link both universes. If Colonel Broyles had uploaded the device into the Machine, Jones could do something much worse: Collapse both universes.