We open on a ship out at sea, and First Mate Gunnarson, who's just had his girlfriend break up with him via e-mail. Unfortunately, his day gets a whole lot worse when a glowy noisy shapechangy space-ship thing appears off the side of the ship and all hell breaks loose. Meanwhile, crisis management expert Molly Caffrey and her ugly, ugly dog, Monster, get called in by the deputy National Security Advisor because some plan she wrote, the titular Threshold, has been activated. Satellites tracked the UFO changing course several times before it disappeared. So she's teamed up with tough guy Cavennaugh, a top biologist by the name of Nigel Fenway (played by Brent Spiner), physicist Lucas Pegg, and a linguist/mathematician/sleazeball Arthur Ramsey.
They fly out to the ship, where they find half the crew dead, and the rest missing. At least until Gunnarson shows up and tries to kill one of them. He's captured and examined, but there's more to come - the crew took a video tape of the craft, and watching the tape causes Molly, Lucas, and Cavennaugh to be seriously affected: you know, the usual, bleeding from the nose and ears, changes to their theta waves, bad dreams... Meanwhile, Ramsey's analysing the fractal pattern that shows up everywhere and Nigel's got mystery blood cells that look like they've grown fur. Cutting their investigation short, a North Korean sub shows up, forcing them to evacuate and blow up the ship, but not before Gunnarson makes an escape, getting shot four times but still jumping over the side of the ship and disappearing into the water.
Nigel gives our team members a clean bill of health (except for the theta waves), but that doesn't stop them having weird dreams about seeing someone who looks like them but isn't them and a forest made of glass with a weird alien thing in it. But Molly's evening gets even better when Gunnarson shows up at her house trying to kill her and mumbling nonsense. The FBI surveillance saves her life, but Gunnarson, who's now been hit by a shovel and knocked into a storm cellar, manages to disappear from a sealed room. The bugs in the house at least give Ramsey something to do, decoding the insane mumblings into "You're One Of Us." Probably not what Molly wants to be hearing.
Tracking Gunnarson to a water treatment plant, they get fooled by one of the other crewmen whose gone to great lengths in his disguise - he shaved! Our crack team almost deserve to lose don't they? Anyway, back at base Lucas has discovered that certain elements of the audio signal that the spaceship gave off have an effect on rats, or at least those that were on the ship and previously affected. Perhaps they can use this signal to lure the missing crewmen?
So here they are - the scientists in a van together, and Molly and Cavennaugh in some plant surrounded by sharpshooters, with speakers set up playing this little bit of the signal. Lucas has a dream about Gunnarson, just before he shows up in person. After a bit of rough and tumble, Cavennaugh shoots Gunnarson and they get their live subject. But the signal's also attracted a hundred or so random people from the surrounding area who don't know why they showed up - and don't show any signs of being changed by the signal. Meanwhile, Molly's blood's pooling into the fractal pattern and the Washington DC traffic is getting gridlocked in the same pattern!
We're in Danville, Virginia and a guy goes crazy in a burger joint, before he goes into the restroom and his face explodes. Yeah, that's going to peak the interest of the Threshold team! So, they go out there thinking they've got another crewman, and instead they've got a janitor from a nearby military school. So how did he become infected? Molly and Cavennaugh get the school, questioning the cadets and taking blood samples for Nigel to test. Meanwhile Lucas and Ramsey get to look at radar from the night of the UFO and find a plane that diverted near to where it flew - there could be a whole plane-load of infectees.
One of the cadets has disappeared before he could be tested. Tracking him down proves fruitless, but does get the headmaster killed when he tries to confront someone trying to hack the school's internet connection with a laptop in the library. And then Molly gets confronted by an older boy, Jenklow, and his squad of cadets, all herding her in the library. She escapes into the basement, and finds the missing student hiding in the map room - and he's completely unaffected by the signal.
Meanwhile, Ramsey puts the screws to the pilot of the plane, spotting that he's hiding something. Lucas decodes the black box and finds the fractal pattern on it, and one of the students at the school was on the flight manifest. The pilot cracks and admits he'd been drinking before the flight, but didn't hear anything out of the ordinary. Molly questions the boy who was on the flight and discovers his laptop has a recording of the alien signal on it, and that the dead janitor was trying to fix the computer for him. Jenklow was also in on the repairs. They knock out the power to prevent the signal being emailed out, but can't find the kids until they discover the school is honeycombed with old steam tunnels.
A trip into the tunnels, and the pressure's on, because the kids have started the school generator. Jenklow's escaped back into the library, and Molly goes to confront him. Meanwhile Cavennaugh confronts the rest of Jenklow's squad by the generator, prepared to defend themselves. But he's quick off the mark, spotting they aren't infected, and persuades them to stand down. Killing the power should solve everything... oh, no, wait, Jenklow had a laptop, and laptops have batteries! Fortunately Molly's aim's improved, and she shoots the laptop to bits before they capture Jenklow alive (even if they come up with a heroic cover story of his death to tell his father).
A man's escaped from a mental hospital, and ignoring the orderly and security guard with their heads twisted right round and the hole in the electric fence designed to kill a man, the escaped patient's room is decorated with pictures of the glass forest. And so our team swing into action, examining the patient's life and his recent behaviour for signs of how he could have been affected by the signal. He was in the hospital because as a young child he killed all his family, burning their house down with them in it. He claimed at the time that they were already dead when he set light to the place, but no-one believed him.
Anyway, turns out that one of the crewmen was there - he left some blood on the fence to give them a handy clue. The escaped patient has broken into a woman's apartment, taking her hostage, and digging through the floor, but he needs a shovel, and going out to get one gets him picked up by Cavennaugh and his agents. Testing him, they find no DNA anomalies, but he's clearly been exposed to the signal if his dreams are anything to go by. Digging up the family's bodies, the team discover that they were more seriously exposed, and questioning the patient, find out that an object was dug up in the back garden - a metal fragment that gives off the same signal.
When they brought it in the house, all the adults started changing, while the patient himself was too young. When his father came at him with a knife, he defended himself, escaped, and set the house alight. And now he's leading our team on a wild good chase to divert them from the real location of the object. Meanwhile, the crewman, having followed him to the girl's apartment, is continuing to dig. Fortunately, Ramsey and Lucas can use the patient's drawings of his house and old geological survey images to track where the house was and get to the apartment. They save the girl, take the object and the crewman into custody, and go on their merry way...
The Baltimore police department confront a couple of thieves at the dock. One gets taken into custody but the other survives being shot, breaks the neck of one of the cop and escapes. Turns out he's one of the missing crewmen, and the Threshold team want some answers. The crewman, Park, was stealing top-of-the-line microchips, powerfully enough to potentially recreate the signal if he could get enough electricity for them. Meanwhile, a trio of Indonesians have been smuggled into the country, probable terrorists.
When they discover Park's in the custody of the Baltimore PD (the dead cop's partner wants payback), they go to collect him, but DHS gets there first, and won't give him up until he tells them where the Indonesian terrorists are. Molly realises that the only way to get DHS to play ball is to find the terrorists first, and so they're hunting for a guy who needs asthma medicine. Lucky for them, the terrorists need to take a washing machine apart for the timer, and are easily caught in a laundromat. Unluckily, DHS manage to let Park escape from their custody. Meanwhile, Lucas is dealing with rapidly improving vision and hand-eye coordination - is his DNA going to start changing next?
Tracking Park by his belongings, they stake out the Baltimore subway, but in another stroke of luck, Park knocks out a section of track trying to draw power from it, and the agents close in. He's got his signal generator hooked up to the rail, drawing power ready to emit the signal. And Lucas can't knock it offline in time. Cavennaugh catches up to a fleeing Park and stuns him, but the combination of the stun gun and falling onto a live rail manages to kill him. Meanwhile, Molly borrows the Baltimore cop's gun and finishes off the generator just in the nick of time.
The signal gets played over the DJ station at an underground disco, affecting everyone there. This could be a worst case scenario for the Threshold team, so they fly out to Miami to find out what happened. Luckily for them, the club-goers have elevated theta waves but no genetic mutation, not having been exposed for long enough. However, the DJ is missing, and she may still have a copy of the signal. Everyone was invited to the disco via a text message, and via some technical wizardry, they track the promoter, and get the name of the DJ.
Said DJ is struggling with some changes of her own. Ignoring the abusive boyfriend who she throws out of a window, she knows something's happening to her (the carpet picnic of sweets and other unhealthy foodstuffs might be a clue!) but doesn't seek medical attention for her troubles. Instead she spends most of the episode wandering the streets looking feverish. The team eventually track her down, buying more equipment so she can DJ another club, and discover her body is still fighting the changes. The signal itself, now on her MP3 player, came from her brother, who was a crewman on the ship and died during the encounter with the UFO - but was on the phone to his sister at the time.
Unfortunately, said copied signal, now in MP3 form, has been infecting any electronic device in the vicinity - mobile phones, credit cards with chips on them - and now it's got into the banking system via an ATM. If it learns how to spread on its own, they could have a worldwide crisis. So what do you do when you've got a rogue computer virus loose in Miami? You pull out the biggest EMP in existence, blame it on sunspots, and black out the city! Not exactly subtle are they? The girl though? She loses her battle - Nigel's experimental drugs don't work and she's added to their motley collection of people in cells.
Lots of people in Rhode Island are having dreams of the glass forest. But there's been a leak of classified information to a reporter, and Molly and Cavennaugh have to follow that up, so Lucas and Ramsey get to fly solo. A fish restaurant seems to be the link connecting all the affected people - is it the fish? Trying to get a DNA sample from the busboy sees him run for it, so perhaps he's their infectee link - the fact that the hands of his watch are bent into the fractal pattern might be a clue.
Meanwhile, the leak has attracted the attention of a Senator, who barges his way in determined to find out what's going on. The National Security Advisor decides the only way to keep him quiet is to bring him up to speed on the programme, and Molly has to give him a tour. The leak itself seems to point to Nigel - the reporter had notes with the initials NF on them - but Dr. Fenway protests his innocence and Molly believes him. Turns out Nigel's been breaking protocol, going to the same bar every night, and someone's bugged the place.
Ramsey and Lucas catch up with the busboy, just after he's robbed a bank, and he takes them hostage. Luckily for them, he isn't an infectee, but Lucas's weapon is charged to take one down and it'd kill a normal human. But channeling the charge through a chair solves that problem, and another examination of the restaurant finds a chunk of driftwood that used to be part of the ship. That problem solved, leaves us with two others - the bug turns out to have been planted by a private investigator hired by one of Fenway's former wives, and Cavennaugh puts paid to his little scheme. But the nosy Senator has stolen a copy of the signal, listened to it (killing his aide in the process), and now intends to play it on a plane with the National Security Advisor. Unfortunately for Molly, she's too late to stop him, and has to order the plane shot down.
New Harmony, Indiana. Do they keep lists of these ridiculously named US towns just for such an occasion? Unfortunately, this one is the home town of one of the infected crewmembers, and the agents they had watching his house haven't checked in. Flying out there, Molly and Cavennaugh discover a priest preaching about glass trees and the creature that lives amongst them - has he been exposed to the signal perchance? More digging gives them the crewman, Sontag's, mother, who plays sweet and innocent and claims not to have seen her son. Which doesn't really tally with the priest, who claims the guy came to him in a dream.
But testing Mrs Sontag shows that she's unchanged genetically, so more digging is in order. And after more questions to the priest (and his spiffy stained glass window with the fractal pattern in it) Molly discovers really creepy cabbages growing in the church garden - cabbages which have human teeth in them! Confronting Mrs Sontag, she effortlessly dislocates Cavennaugh's shoulder - but hold it, wasn't she uninfected? Turns out we've got a rogue agent on our hands, and he takes out Molly at the church, chaining her in the basement for Sontag to experiment on.
Sontag's using his own blood - as a fertilizer to grow weird plants, and as an infection agent - as evidenced by the second missing agent, deformed and dead alongside Molly. Sontag takes the opportunity to gloat and tell Molly everything, but Cavennaugh's seen through the rogue agent and shows up to save the day just before he can stick Molly with his blood. Meanwhile, Lucas and Ramsey have been surveying the wreckage of the ship, and it's growing quite the crystalline forest down there at the bottom of the ocean. Oh, and that North Korean sub that was about to discover the ship back in the pilot, its wreckage is down there as well - so who got the sub?
Three separate women - one explodes at a hot-dog stand, one punches her way through a bank window and assaults the teller, and one rips her husbands head off. They're infectees, but what's the connection? Meanwhile, the President's picked a new National Security Advisor, so Molly has a new boss - one who wants to get his hands dirty tinkering with her plan. You know, most of this episode is dull computer work with Lucas and Ramsey backtracking a whole bunch of payments to a Caymen bank account and then the withdrawal of that money and its shipment to Mexico.
More importantly though, the three women were infected at a fertility clinic - one of the missing crewmen donated his sperm and they were infected by it. And one of the women is now pregnant with a foetus growing at a vastly accelerated rate. What do Threshold do with an alien baby anyway? Nigel wants to chop it up to learn from it, but Molly seems reluctant on that point. Foolish, foolish woman. Anyway, the woman who assaulted the bank teller is the trophy wife of an exceedingly rich friend of the President, so she's going to get to skate.
Well, almost - she throws a charity ball, and Molly and Cavennaugh go to capture her there, but she slips out. Fortunately, Cavennaugh's sneakily planted tracking device leads them to Mexico, where he manages to get himself captured while trying to decide whether to shoot the woman's double. Fortunately, Molly shows up and takes out the woman, and they track one of the other crewmen to a cabin nearby. But he's no longer there - he's taken the half-a-million dollars he's collected and flown to DC with them... and he's a former Navy Seal with intelligence training, so he's probably not going to be a pushover to take out...
The infectee prisoners stage a gaol break when one of the guards becomes sloppy. Cavennaugh recaptures them, but it ups the priority on moving them to the newly finished detention facility. Meanwhile, it turns out the guard wasn't being sloppy - he's become infected somehow and hallucinated that he had another guard present with him! Molly's new boss insists that the infectees get moved in one shipment rather than the five separate trips she was planning - this isn't going to go well is it?
Molly comes clean to the infected guard, telling him what's going to happen and asking him if he'll talk them through the changes as they occur so they get some more data - in return he insists she kill him before he's completely changed. Molly's water delivery guy turns out to be a former Seal who was dishonourably discharged for striking his superior. A superior who just happens to be the captain of the ship and the chief infectee. But the water guy wasn't infected.
The transportation convoy is indeed hit by the infectee, Manning, en route, and although Cavennaugh manages to secure the prisoners, Manning gets away with Agent Hayes, who turns out to be Cavennaugh's brother (and, we subsequently discover, is now infected). Molly and Ramsey carry out the promise to put the guard out of his misery. And Lucas, who's clearly been under some stress, has been hallucinating that he's got an assistant - his theta waves are off the charts and he has to be relieved from duty until they can work out what's going on. Oh, and the guard who was mysteriously infected? Turns out it was something he ate!
So, Lucas is infected. And there's something in the food supply. Clearly they need a botanist to help with the plant analysis, and you can't go wrong by recruiting Catherine Bell (playing Dr. Daphne somethingorother) for the job now can you? Manning calls, wanting a talk with Molly - apparently he's got some information for her. Meanwhile, they have to question Lucas's wife as to how he got infected. You know, being a vegetarian when the aliens can grow infected vegetables? Not necessarily a smart move!
So, it's the tomatoes, and the nearby farmers' market bags them an infectee. Backtracking the blood-drained corpses from the prior episode gets them to some farmland in Indiana, not all that far from where Sontag was performing his experiments at the church. Seems our new NSA transferred the agents off Molly's search for more plant experiments for some other purpose. Ramsey isn't handling Lucas's infection all that well, drinking too much and playing online poker during work hours.
Cavennaugh and Daphne track down the plants and cut off the supply. Nigel comes up with a hail-mary idea to save Lucas (of course he does), playing a burst of the alien signal to somehow stop him changing. Huh?! Won't that make the problem worse? Apparently not, and it causes Lucas to have a dream about a civil war era guy who apparently stopped a bunch of alien infectees back then... and he's got a journal hanging around somewhere if they can just track it down. Ramsey's calculations put the number of people infected by the tomatoes at about 190. Which means Threshold has to step things up - everyone now gets their own team of people to boss around which should be entertaining, if hard to keep track of.
Ramsey spends the night with a stripper, but it's interrupted when a superstrong guy breaks in and kills the girl with some weird instrument. He's clearly an infectee - but according to a DNA check of cells under the girl's fingernails, he's only partially changed. The girl however, is fully changed, which kinda freaks Ramsey out. A mixup with the FBI turns up the fact that the girl isn't his first victim - he's killed four others in the same fashion... and one of them doesn't show any mutation.
He does however show elevated theta waves, even in death, so he's clearly been exposed. The weird instrument leads them to the conclusion he's a doctor, which makes Lucas' trip to visit his wife at the hospital a little silly. Luckily, Cavennaugh shows up to chase him off, and Lucas has to persuade his wife that his job is worth it - it's even worth his life. Having a lead on Dr Sloane allows them to search his house, where they find surveillance photos of a bunch of infectees, including Manning.
Sloane confronts Molly when she steps out for coffee, but she persuades him that although she was exposed, she's not mutated, and he seems to buy her story - at least, he leaves her alive. Via some clever detective work, our team track the photo of Manning to a water bottling warehouse and they send a team in. Sloane's there - being in time to save Molly's life, and she lets him go in return. Meanwhile, Cavennaugh gets Manning, but there's no sign of Agent Hayes. The bottled water was contaminated - but they suspend shipments so hopefully that plan is stopped. Sloane leaves Molly a coffee on her night stand to make up for the one she dropped when he assualted her. And Ramsey's drinking problem is getting out of control...
They've tracked a number of those infected by the tomatoes, but one fled the city with a couple of cratefuls of the fruit, and travelled to Allenville, Virginia, where his father, a noted physicist has a house. Meanwhile, the pregnant infectee goes into labour. Nigel, Ramsey and Lucas get to stay behind and look after the birth, while Cavennaugh and Molly play the happy newlyweds looking for houses in Allenville. Their first stop - the two agents they had in town... except a woman's feeding their bodies into a woodchipper when they get there. Taking our their first infectee, and having no cellphone signal, they head to the town diner to use the payphone (unfortunately out of order) and get their second surprise - the whole town is infected. It's a good job Molly and Cavennaugh have been exposed to the signal...
Having to eat a really large free steak to maintain their cover, they then head out to the home of the physicist, where they sneak into his lab and look at whatever it is he's building. But his son comes home and they have to stun him. He does start them down the road of progressively damaging their car in increasingly amusing fashion though. Oh, and the guy leading the infectees in town - Agent Hayes... Molly makes a smart guess that they're using the local stables as their base, and discover something being built: some sort of signal generator. Which Cavennaugh gets the job of destroying.
So, a bit of shopping, a couple of gas canisters, a working payphone so they can get a message to Baylock, and they're all set. Meanwhile, back in DC, the woman gives birth to a perfectly healthy, human, baby. She's rather insistent that she gets to breast feed him, so much so that she escapes from her restraints and chases Lucas and Ramsey throughout the building in her effort to get to the boy. Nigel finally stops her and discovers her breast milk is extremely infectious. Molly and Cavennaugh confront Hayes, and take him prisoner, but the rest of the town are on their tail so they leave him (Cavennaugh wants to shoot him but Molly stops him... very silly) and luckily run in to Baylock and a whole bunch of agents. Hayes is gone when they get back to him. Oh, and in a dream, the newborn boy comes to Molly several years later to tell her that her plan worked... but she's not around to see the results...