Samantha Carter is awoken at 2 o'clock in the morning by a phone call. The man on the other end identifies himself as Dr. Flemming, and tells her that Adrian Conrad's secret project never ended ("Desperate Measures"). Flemming races down a road, but is followed and run off the road. Carter hears a crash, and the phone goes dead.
The next morning, General Hammond informs her, Teal'c and Jonas Quinn that Dr. Flemming's car was found wrecked, but that there is no trace of him. He was an employee at a biotech firm in Steveston, a small town in Oregon. The company is Immunitech Research, owned by Adrian Conrad (the man who once kidnapped Major Carter before he was voluntarily implanted with a Goa'uld symbiote). With a potential connection to the Goa'uld that has taken Conrad as its host, the team travels to Oregon to investigate.
They can't wait for Colonel O'Neill, who has recently been blended with a Tok'ra symbiote to save his life ("Frozen"). The Tok'ra haven't found a new host for the symbiote yet, and O'Neill remains off world. Carter is put in command of SG-1 for the Earth-bound mission.
In Oregon, the team learns a lot from the local sheriff. Immunitech burned to the ground the night before, destroying Flemming's lab. It's a big hit to the small town, which relies on the company for many jobs. And Flemming isn't the first disappearance. His partner, Dr. Peter Stoeffer, disappeared two months ago, also under mysterious circumstances.
The team heads to Flemming's home, but find that it's been pillaged for any and all valuable information. But while they are there, the team gets a break: a package is delivered to Flemming, from Flemming. Carter opens it, and finds a syringe filled with an unknown liquid. She sends a sample to be analyzed, and preliminary analysis indicates that it may be a sulfur-based antibiotic.
Teal'c and Jonas begin to notice that the townspeople are acting strangely. They nearly get into a bar fight one night, but the next morning they encounter one of the men from the bar -- who claims to know nothing about it, and tells them that he was home asleep. Jonas observes that the entire town seems to be walking around as if they're half-asleep.
What was the purpose of Immunitech's research? SG-1's investigation reveals that Flemming and Stoeffer had been studying embryonic stem cell research, which could potentially be used in cloning.
When Sam mentions that the biotech firm saved the town after the local shipyard went out of business, Jonas (who seems to have a photographic memory and keen powers of observation) remembers seeing tire tracks in the snow when they passed the shipyard. If it's out of business, who has been visiting the large, abandoned building? SG-1 checks it out, and finds an enormous, partially-constructed space craft inside.
They also find several computer discs, and take one. In their hotel room, Carter works to crack the encryption code. When night falls, Teal'c and Quinn return to the shipyard to see who arrives.
What they find is nearly the entire town -- dozens of people arriving to work on the ship. But they are quickly apprehended -- not by the townsfolk, but by undercover N.I.D. agents. On the way back to the hotel, Agent Singer tells them that the N.I.D. knows what's going on in the town, and has been monitoring it.
Immunitech was cloning Goa'uld symbiotes -- but the creatures began taking over the local townsfolk. They are still infants, and so they are strong enough to take control of their hosts only when the people fall asleep at night. They are building a ship to escape Earth, and the N.I.D. plans to seize it when they are finished.
But the local sheriff is one of the Goa'uld, and he leads a group of Goa'uld-infested citizens to the hotel. Carter unlocks enough of the computer disc to see that the data is written in Goa'uld, and begins to figure out what is going on. When the Goa'uld arrive and break down her door, she injects herself with Flemming's antibiotic. She is infested with a young Goa'uld, who takes control of her.
Teal'c, Jonas and the two N.I.D. agents are also soon captured. Led by Major Carter, the agents are given their own Goa'uld. They are sent with the remaining cloned symbiotes to infiltrate the N.I.D., now that the organization has been called in to break up their secret operation and seize the ship.
But Carter is not truly under the Goa'uld's control. The antibiotic acted as an immunity and killed the symbiote (which was genetically engineered with a specific kill-switch, activated by the drug); Carter then played along to gain their trust. She zats the entire group unconscious, then follows the Goa'ulded N.I.D. agents and apprehends them as well.
The ship is confiscated and sent to Area 51 where, though only partially complete, it may still prove valuable. The entire town is treated with the antibiotic, which kills the Goa'uld and leaves them all with no memory of what had happened.