In Boston, a man named Neil buys a cafÃ© mocha inside the Clane Center before getting on the escalator and heading outside. He drops his drink, clutches his stomach and drops to his knees. A woman passing by asks if he’s okay. Probably not: smoke starts pouring off of him and coming from his mouth, which has turned black. The same thing happens to other people. One woman cautions another not to move, as that is what seems to be causing the deaths. Several other people stand frozen in place, afraid to move a muscle.
After the credits, Peter is reading real estate listings to Olivia as they lie in bed. She suggests they look for a place with a nursery. They kiss, but the sweet moment is interrupted as both their phones start ringing.
Folks in hazmat suits examine the victims, some of whom are still smoldering. Walter barks out orders from his spot behind caution tape. He complains that Astrid is “mother henning” him as she fusses over his coat. She tells him to humor her. The air is declared free of airborne toxins and Walter eagerly rushes over to examine the bodies. The living commuters plead for help. Inside, Broyles explains to Peter and Olivia that at 3:23 pm, over two dozen people apparently died from spontaneous human combustion. Peter says that’s just a myth, because it’s not like he deals with weird shit on a regular basis or anything.
Walter examines one of the bodies inside the building. He seems to be enjoying his work until a woman – hey, it’s Charlotte, from Lost! – asks if she’s going to die. Walter says he can’t say, and after some confusion on his part on whether or not she’s an alien, he explains that he’s a scientist. Charlotte allows Walter to take a blood sample. He notices smudges on her fingertips, which she thinks may have come from the escalator rail.
Using a mobile lab, Astrid confirms that there’s something foreign in Charlotte’s blood but she can’t say what until they get back to the Harvard lab. Walter wonders how the contaminant is staying fresh if someone smeared it on the escalator and people keep touching it. His attention is drawn to a machine installed in the escalator that’s generating nanites. The nanites are being activated by biokinetic energy and the longer they stay in the bloodstream, the more sensitive they become. Walter insists he needs to get one of the living victims back to the lab. After confirming that her family will be provided for if she dies, Charlotte, whose name is Jessica Holt here, volunteers.
After the break, Walter and Peter are at work on a cure while Astrid monitors Jessica’s vitals. Jessica tells Olivia she’s a night-shift ER nurse, so she’s seen her share of weird. She asks for a phone, and does an awful hell of a lot of moving around while she calls her kid’s father. She asks him to pick up their daughter, Sarah, after school, and he agrees (after protesting a bit because it’s not his day). Olivia sees a picture of Sarah on Jessica’s phone, in case it’s not clear that she has a little girl.
Walter’s not sure how much longer it’s going to take to finish making an antidote. Jessica’s temperature starts rising rapidly. Walter tells Olivia that an ice bath won’t help, and asks her to keep Jessica calm. Olivia takes Jessica’s hand to calm her down, as her temperature gets as high as 105 degrees. Olivia focuses on her and is able to bring her temperature back to normal, and knock the power out for a few seconds. Olivia has no idea what just happened.
Peter gives Jessica an injection to neutralize and flush out the nanites. Walter theorizes that Olivia used her Cortexiphan-based telekinesis to slow down the molecules in Jessica’s blood enough to bring her temperature down. Olivia walks Jessica outside, where a police car is waiting to take her home. Jessica explains that she volunteered to be Walter’s guinea pig because her daughter needs her (and, “Her father’s an idiot”), just in case it still wasn’t clear that Jessica is a mother. Olivia gives her her card and sends her off.
Broyles calls Peter and Olivia in to view CCTV footage of David Robert Jones tampering with the escalator. Unfortunately, the cameras were unable to catch him after he left. Olivia wonders what nanites have to do with Jones’ doomsday plot. Peter is sure that whatever he’s planning, he hasn’t given up just because the bridge is closed.
At the lab, Walter recognizes the design of the nanites as the work of William Bell. Meanwhile, DRJ strolls into a room on what looks like his freak show freighter, where none other than Bell is waiting for him. DRJ reports that Olivia bested them. Bell and his awful hair laugh and tell him, “Don’t be so sure.” They look at a chess board, on which Bell’s been playing the same game for years. Evil geniuses love some chess. Bell tells DRJ he has to be willing to sacrifice “a bishop” to win the game. Jones says he’ll get right on that.
Walter tries to convince Olivia and Nina that Bell is alive. Nina reasons that DRJ had access to Bell’s notes when he worked at Massive Dynamic, so maybe that’s why the nanites look like Bell’s work. She remarks that Bell died seven years ago on Christmas, which Walter finds upsetting. He thought Bell died on New Year’s Day, because he visited Walter at St. Claire’s the night before to say goodbye. Nina is also upset, and confesses that Bell had lymphoma and crashed his car on purpose. She says she saw his body, and besides, he wouldn’t want to do something like collapse the universes.
Walter is determined to prove Bell’s alive, so he gets Peter and Olivia to take him to St. Claire’s. A janitor taunts him, asking if he’s returning as a visitor or a patient. Walter is clearly upset by this. Peter takes him in to speak with the administrator, a Dr. Benlow who looks kind of like Jennifer Garner’s broke sister. (In real life, she’s John Noble’s daughter, Samantha.) There’s no surveillance footage from the time in question, but they do get to look at the visitor logs. Walter thinks they look a little too perfect. Olivia gently asks if maybe all the shock therapy made Walter hallucinate Bell’s visit but he’s sure it really happened. Then he starts sniffing the hell out of (and licking) the log book, and asks if he can take it. Benlow reluctantly agrees, as it’s already been digitized. And licked.
At Peter’s, Olivia accidentally cuts herself while slicing garlic. She’s thinking about how close Sarah came to losing her mother. Olivia wonders if she and Peter have any business having kids, given their dangerous line of work. She’s also worried about how her abilities are developing. Peter tells her everything’s going to be okay. Then they notice a bright light outside in the night sky. Elsewhere, Broyles’ attention is also drawn to the shaft of light. It comes down from the sky and starts drilling through a building nearby.
After the break, Peter and Olivia are en route to the light’s target while Walter (still in the lab) explains that DRJ must be bouncing the sun’s light off of something and turning it into a death ray. Astrid, meanwhile, is accessing satellite imagery and researching Beacon Hill geological data simultaneously. Every workplace could use an Astrid or two.
It becomes clear that DRJ is drilling down to the a recently discovered oil reserve under Beacon Hill, which if hit by the sunbeam would set Boston on fire. Walter tells Peter to have Broyles evacuate the city. He directs Peter and Olivia to turn around, and head to the location from which DRJ is transmitting two signals to the satellites. Peter and Olivia soon reach the location, two buildings directly across from each other. They split up with walkie-talkies to turn off the satellites, as Jones watches from a car nearby.
At the lab, Walter does “¦ um “¦. science (lemon cake incubator + pig brain + tissue-regenerating Cortexiphan) in hopes of revealing Bell’s fingerprints on the log book. The prints that appear are smudged, but Bell also left behind Chilean almond oil from his favorite imported snack. Walter wants to go to the nut importer to follow this lead. He storns off, then realizes he needs someone to drive him to the warehouse.
Peter instructs Olivia on how to turn off the transmissions, because Peter knows everything. They’re able to turn the sunlight off, but then DRJ shows up and starts beating Peter with a shovel. Olivia can’t get a clear shot, then loses her gun to some gung-ho rent-a-cops (who don’t seem too interested in helping Peter). So Peter’s getting his ass handed to him (seriously, how are you Mr. Mary Sue one minute and completely useless the next?) until Olivia uses her telekinesis to fix Peter’s dislocated shoulder (ouch) and help him defeat DRJ. The look on Peter’s face after “he” wins is kind of thanks, goddammit what the hell? Anyway, Jones gets knocked into some electrical wires. He says, “I got it wrong; I was the sacrifice,” before half his face crumbles into dust. Way to Die Number, what? 8,705 on this show?
Down by the harbor, Walter lets himself into A1 Imports. A guy named Tom says the company went out of business a few years ago. He’s called away by someone on a walkie-talkie. Walter wants to “ask around” the apparently empty place but Astrid noticed Tom had a gun and is ready to get out of Dodge. Then a loud noise draws Walter’s attention, and poor Astrid is left to follow him into a large room filled with metal containers. Oh good, the shipment of bio-engineered hybrid monsters has arrived. Walter and Astrid are confronted, and then chased, by Tom and his friends (who also have guns). Astrid is able to take one of them out but then she gets shot in the stomach. (Who else yelled “No!!” here?) She falls and Walter cradles her body. Then Bell and his hair come creeping out of the shadows, all, “Hello, old friend.”
On the second half of the season finale: Jessica Holt returns, Bell’s been planning Something Big for quite some time, and somebody gets shot. Probably. Still no word on Astrid, though.