In Paris, Delavane contacts Chloe and says that the team is heading to Pendar Island, Massachusetts. He explains that two weeks ago a cargo ship went from Oslo to Portland. The crew complained about a high rat population, and 48 hours into the journey the crew reported that the ship had become infested. Eventually the shift ended up adrift near the resort community of Pendar Island. A fisherman has claimed that he saw thousands of rats swimming ashore, and the authorities found the crew dead, killed by rats. In the cargo was grain treated with pesticide created by Reiden. Delavane wants the team to go to Pendar Island and determine if a containment process is necessary, and to bring back one male and female rat for analysis.
The team arrives in Boston and Mitch plans to stay behind to contact a friend at Harvard. Jamie reluctantly agrees, and Mitch calls Clayton and says that he's in town and has the Mother Cell, and they should arrange a meet for later that day.
On the boat to Pendar Island, Jackson suggests that the Mother Cell is an accelerant, and that the rats multiplied aboard the cargo ship. They worry that the rats were only the first to reproduce because they have a short gestation period, and humanity could be overwhelmed if lions, crocodiles, and other animals swarmed. Chloe insists that they need to capture a male and female so they can determine how the Mother Cell affects reproductive behavior. Jackson points out that the crew was eaten by rats, and warns that rats that taste human blood crave it. Abraham talks to Jackson privately and asks what is concerning here, and Jackson explains that his family vacationed on Pendar Island when he was a kid, before Robert got bad. His last good memoires were on an island that appears to be overrun by bloodthirsty rats.
Mitch visits Audra to pick up Clementine, and asks if Clementine's dog Henry has been acting aggressively. Clementine comes down and says that she doesn't remember Mitch, and Mitch says that he remembers her. Audra realizes that Mitch hasn't planned anything to do, and says that he planned to improvise. She suggests that Clementine take Mitch to her park and goes to make a picnic lunch, and Clementine goes to get Henry's leash.
On Pendar Island, Jackson and Chloe approach Sheriff Rebecca Bowman. Rebecca knows Jackson from when he vacation there and assumes that Jackson and Chloe are together. They correct her assumption and explain that they want to talk about the rats. Rebecca says that the fisherman, Billy T., has a vivid imagination and drinks heavily. She says that there's nothing to be concerned about, and doesn't believe that the rats killed the crew. The coroner believes that a carbon monoxide leak killed the crew and then the rats ate the crew.
Jamie and Abraham go to a nearby café and Jamie complains that Mitch hasn't responded to her texts. Abraham says that she should avoid meeting with any law authorities.
Jackson tells Rebecca that they should evacuate the island, but the sheriff warns that it would cause a panic if they evacuated during peak tourist season. She tells them that some rats were spotted near the Wilson Hotel, which is being renovated, and suggests that they get together later. Once Rebecca leaves, Jackson tells Chloe that the hotel is huge and would make a perfect breeding ground for the rats.
An exterminator, Jerome Pratt, is at the Wilson and spots a rat. He follows it into an empty room and hears it in the overhead ceiling. Jerome sets up a ladder and climbs up, and hundreds of rats swarm onto his head.
Later, the team breaks into the hotel and discovers that the traps that Jerome left are untouched. Abraham has brought special traps to capture a male and female without harming them, Jackson and Chloe check the upper floors while Abraham and Jamie plant the traps on the lower floor.
At the park, Clementine explains that Audra only lets her come alone to that park on her own. Mitch gives her an old parking ticket and explains that he got it on the day that Clementine was born. He was late getting there and parked illegally, but he made it there on time. Mitch has saved it for ten years and Clementine appreciates the thought.
In New York City, Ronnie "Dogstick" Brannigan goes on a date with a woman, Ginny. Her phone ring but Ginny refuses to answer it, assuring Ronnie that it isn't an emergency.
Abraham and Jamie discover that the wires at the circuit panel are sheared through. She's still unable to get Mitch, and is thrilled that they're close to getting Reiden. Abraham points out that he and his cousin Simon looked for a rare antelope and found a small herd. But afterward they found an emptiness because they had achieved their goal. Jamie says that there won't be any emptiness for her when they bring down Reiden. Abraham gets the power up, and Jackson and Chloe hear thousands of rats sharpening their teeth.
Jamie and Abraham check the traps and find one with a male rat inside. Jackson and Chloe arrive and Jackson calls Rebecca and tells her that the hotel is infested with rats. She says that she's coming and hangs up, and Jackson says that they have to find the female rat and get out.
At the park, Mitch and Clementine eat Audra's picnic lunch and Clementine wonders if Mitch has a wife or girlfriend. He says that he doesn't, and Clementine admits that she likes Justin. She assures Mitch that she doesn't call him "Dad," and Mitch asks how she's feeling. Clementine says that she's not feeling bad for a dead girl, and points out that the other girls call her that.
After dinner, Ronnie checks his phone and tells Ginny that a comrade of his, nicknamed "Number 12," vanished. He explains that the comrade is a protégé. Ginny asks what he does for a job, and Ronnie says that he settles differences. Ronnie worries about Number 12 just as a carriage driver, Tim, offers them a ride. As they get into the carriage, the horse starts acting up.
As the team explores the hotel, the lights go out briefly and the elevator comes up. Thousands of rats pour out of the elevator and Jackson, Abraham, and Jamie flee into a room. They get the door closed and realize that Chloe isn't with them.
Ginny and Ronnie take the carriage around Central Park, and Tim asks how long they've been together. Ronnie checks his phone again and admits that he hasn't heard about his friend, and the horse starts galloping. The driver is unable to stop him, and is knocked clear. Ronnie gets Ginny out of the carriage and the horse runs into a food truck.
Mitch brings a sleepy Clementine home, and she tells her father that it was a good day. He tucks her in and Clementine says that he should come along more often. As Audra watches, Mitch agrees.
Rebecca arrives at the hotel and calls to Jackson, but gets no response.
Abraham confirms that they're clear and the trio goes out into the hallway. Jackson is unable to raise Chloe on the phone. They check the bag and discover that the male rat has given birth. Jackson confirms that all of the offspring are males, and tells Jamie that it's statistically impossible for a litter to be one sex. He speculates that all of the evolutionary mutations that they've seen are to destroy humanity, not to improve the individual species, and the trio continues searching for Chloe.
Rebecca spots a rat and follows it into the room where Jerome's corpse is laying on the floor. Chloe comes in and says that they need to find something better than traps to deal with the rats.
Mitch asks Audra to keep an eye on Henry and put him in his crate if he becomes aggressive. He warns his ex-wife that animals are acting strange and to call him, and she wonders why she should call him about anything. Audra figures that he's having a mid-life crisis and says that she doesn't need him there, and Mitch agrees. As he goes, Audra asks him why he's back now. Mitch leaves without answering.
As they search for Chloe, Jackson suggests that the grain on the cargo ship accelerated the rats' reproduction cycle. Once the ship was no longer safe, the rats sought out the hotel. Jackson realizes that the rat offspring are dehydrated because the males can't nurse, and figures that there must be large female rats in the hotel. Jamie realizes that they are talking about rat queens, and Jackson says that they have to find them.
As the medics take the injured Ginny away, Ronnie says that he'll see her at the hospital. His phone rings and a man, Murph, tells him that Number 12 is dead. Murph says that Number 12 was shot and his body was found in a hotel stairwell and Alabama. He sends the hotel security footage to Ronnie, and Ronnie promises that he's going to find out why Ben was in Alabama and who he was with.
Jackson says that the rats must have one big nest, and he figures that it's in the hotel basement. They go there and hear the rats, and find the males swarming around several enormous female queens. As they work out what to do next, more rats drop down and cut them off. Chloe and Rebecca arrive and Chloe uses Jerome's flamethrower on the rats. Jackson yells at her to kill the queens, and she orders them out and burns the fem ale rats.
Later, the fire department arrives and Jackson tells Rebecca that the pups won't last long now that the queens are dead. She figures that there is more going on, and wishes him luck finding it. The sheriff tells Jackson not wait another ten years to come back and as she goes, Jackson apologizes for disappearing and never explaining why. She says that everyone knew what was going on with Robert. As she goes over to hug her boyfriend, Chloe comes over and tells Jackson that he had good taste when he was 12.
Mitch meets with Clayton in his office and Clayton hands over the drug. After a moment, Mitch takes out the Mother Cell… and sees Delavane in the office. Delavane looks over and sees Mitch.