AHigh school kids are out in the woods drinking and goofing around when a bright light flies by overhead and lands. They panic and drive away as a bizarre suited figure staggers away from the landing site and one of the kids shoots and kills it. The teenagers approach it and find a man in an astronaut suit.
Avery, Frank, and Stu show up to check out the death and one of the policemen find some shredded black cloth. Avery calls John in and they head down to the morgue and John verifies the suit is accurate. They get the suit open and determine the man died of cyanosis. They're interrupted when OSI Colonel Dunagan shows up with a Federal warrant and demands the body and all evidence they've gathered. John puts up a brief fight but Avery okays it and Dunagan leaves with everything.
At The Sea, they discuss the case with Digger who hints about all the conspiracy angles. they catch a newscast about the dead man where it's stated he died in a training mishap. John hacks into a spy satellite but the cloud cover is too thick. Digger directs them to a LaCrosse satellite that John can hack into it and they get in and view the image where the body was found. They spot a circular clearing – the same as the one on Horseshoe Island where John woke up.
John, Frank, and Digger brief Avery on what's going on and announce they're going to head off to investigate, even though Avery warns them it could Frank his job. The guys sneak in past the perimeter patrol while Avery goes to the base to talk to Dunagan and demands answers. Dunagan tells her off the record that he doesn't know what's going on and they've already cremated the astronaut's body. He doesn't have much to add and Avery departs.
The guys are driving in when they spot a disk indicating there are thermal scanners in the area. Avery meets with the teenager who shot the astronaut but his mother insists they have nothing to say and Avery realizes the government has talked to them. John uses a fire extinguisher to make laser beams visible and then take windows from Digger's car to deflect the beams and make their way through.
Avery works with Stella to connect the dead astronaut to Roswell and Area 51 before he arrived in Washington. At the base, Dunagan goes into a control room where they're monitoring a team of astronauts who are panicking, and Dunagan insists the mission continue.
The guys find a large metal manmade structure in the forest, labeled Mars Habitat One. John concludes it's designed to test environmental conditions. John manages to get the door open and they find the inside torn up. They also find several corpses, all showing signs of cyanosis. They try to call but there's no cell phone tower in range. The door seals shut as in a control room a man monitors what's going on.
Stella and Avery try to get a lead and Avery talks to Dunagan's staff sergeant at home. The staff sergeant says Dunagan just bought a new car and is planning a trip to the Cayman Islands, but he doesn't know where Dunagan gets the money and he demands Avery leave. Stella can't track the extra money but does track a new corporation under his name that can handle wire transfers.
The guys try to break out without much success and they start sniping at each other. They find a parachute flare that accounts for the lights the teenagers saw. John determines they were stimulating a Mars expedition and the astronaut was running a mission simulation when he went outside and was shot. Digger tries to blow a way out and Frank opens fire, and they're almost hit by the ricochet. The three of them scream at each other until John realizes they're suffering from cyanosis and they only have an hour and a half until they're dead.
Stella manages to backtrack from the IP address on the satellite photo and spot the shelter. With sixty minute left, John determines the recyclers have been sabotaged then uses a transmitter to send a Morse code signal for SOS through the dome light. Stella and Avery pick up the signal which includes the XR-74 – the model number of the recyclers. Avery figures out someone is working with the contractors to make a bundle off the malfunctioning recyclers when a new contract comes up.
Avery confronts Dunagan who takes her to the control room and shows her remote cameras indicating his men are fine and John and the others aren't there. Avery figures out it's a looped tape and they get to the habitat as John hallucinates his arrival on Horseshoe Island. When the guys are apparently dead, the door opens and the staff sergeant comes in. But the guys get up – John fixed the recyclers and they're fine. Avery concludes the staff sergeant has set up Dunagan and killed his own men so he could make money on the contracts. The staff sergeant confesses the deaths weren't intentional but he just got in over his head. And John, Frank, and Digger exchange apologises and rebond.