Worst case scenario expert, Dr. Caffrey, recruits a team of elite and slightly eccentric scientists to determine if an alien civilization has made first contact with the human race. Mysteries abound. Is the alien race trans-dimensional? Is it friendly or malevolent? If friendly, why did the crew members of the ship that encountered the alien kill each other? Is the strange helical symbol an attempt at communication? Are the aliens altering the DNA of human test subjects? And how are the odd dreams/nightmares everyone is having related?

A ship at see comes into contact with a strange light in the sky. The US government immediately sets in motion the Threshold scenario, pulling together the team suggested by Molly Caffrey, crisis management expert. The team which comprises a medical scientist, linguist, mathematician and shadowy action man are yanked out of their lives and whisked off to examine the ship. There they find that all the living creatures have been affected, many showing strange behavioural patterns (as in they create a pattern with their behaviour). The pattern is a fractal and it keeps on occurring. Some of the crew are missing and there is one survivor. He has been turned into a superman and escapes despite being shot in the chest 4 times. It becomes clear that aliens are rewriting the DNA of their victims, turning us into them. The crisis team are the only ones who can figure out how to catch the rest of the crew before they can infect the rest of the world. In the meantime, they have been personally targeted by the 'infectees'.

A new infectee is discovered, but it isn't one of the crew off the ship. He was the janitor of a military academy. The Red Team immediately launch into action and discover that a plane passed the site of the alien appearance and picked up the signal. Later, at the academy, one of the students was trying to get his computer to work again and infected the janitor and one of the older students. That student has one intention, to put the signal onto the internet. That will infect a third of the population of the USA within a week.

An inmate from a lunatic asylum escapes by twisting guards heads almost off and breaking through an electric fence that should have fried him to a crispy state. Question is, how could someone locked up in a cell for 30 years be infected? The answer lies in what happened to the rest of his family and what drove him to lock them in their basement and set fire to the house.

An infectee is caught by Baltimore Police whilst trying to steal microchips being brought into the country. They are specific chips being used to make a very advanced and powerful acoustic device, the kind of device that could transmit the signal and infect others. The question is, where was he planning to set it off. The Threshold team have to find some illegal terrorists to trade for their man with another department, but by that time, their man is gone and there's not a lot of time left to stop him.

A fragment of the alien signal is played by a DJ at a big party. Fortunately, the fragment is too small to have altered the partygoers, but the DJ has gone on the run and there is a greater threat. The signal has somehow got into machines and is spreading electronically.

There's a leak in the Threshold team and the papers are on the trail of Caffrey. A Washington DC senator uses the leak to nose around and a whole bunch of Rhode Island residents have started dreaming about glass trees.

Alien crystals have formed on a plank that showed up in the last episode and the team set out to find the wreck of the original ship to try and track the wreckage. What they find when they finally succeed is the stuff of nightmares for Caffrey. She, on the other hand, has problems of her own as she is licked up in cellar, beaten and bruised with a very dead body nearby.

Three women are identified as being infectees in the Washington DC area. The outbreak seems to be unconnected, but the team quickly locate a fertility clinic that has treated all the women. It seems that one of the crewmen from the original ship is providing infected sperm samples and creating alien babies. Life is complicated by the fact that one of the women is the wife of just about the biggest contributor to the President's election fund. Oh, and the new boss is poking around as well.

The infected food is identified as the source of Lucas's infection. Fenway, though, has some new ideas as to why he is taking longer to mutate than anyone else and a plan that might bring him back from the brink. The source of the food contamination is the new target of the team and they set about tracing the commonalities between the new reports of infectees and what they ate. There is also a new team member to train. Caffrey gets a visit from the leader of the infectees and gets told a story. Does the file from NASA confirm what he said, or refute it?

Ramsey is enjoying a tryst with a stripper when he is rudely interrupted by an alien, but one that kills the stripper and leaves. It turns out that the stripper was an infectee and the man who killed her is a doctor who is only partially mutated and so is able to detect the aliens and kill them, but is not able to distinguish between full infectees and those that have had low levels of exposure such as Molly, Cavvanaugh and Lucas. Information also comes in about the location of the infectees' leader and it appears that he is now after the water.

Molly faces the biggest outbreak yet. One of the infectees makes it back to the very small town on Allenville. Molly and Cavvanaugh go in to investigate and end up posing as infectees when they realise that the whole town is infected and is building a machine to send a message to who knows where. Back at Threshold Central, the others have their hands full when the infected mother to be gives birth and then sets about wreaking havoc when they take the baby away.