The guys arrive in South Dakota in June 24, 1876, near Little Bighorn. They are captured by Indians, although Doug manages to escape and make it to Custer's camp. Custer refuses to believe Doug's tale. Meanwhile, Tony has tried to warn Sitting Bull. The Indians prepare to burn Tony at the stake, but Sitting Bull intervenes, impressed by Tony's bravery. A trial-by-combat settles the matter when Tony wins against Yellow Elk but spares his life. Tony tries to convince Sitting Bull to approach Custer peacefully, much to the disgruntlement and skepticism of Crazy Horse. Sitting Bull lets Tony go to Custer's camp with a message of peace, but Custer refuses it and locks both travellers up. They manage to escape, and are forced to watch as history plays itself out and Custer and his men are massacred.

The guys arrive in Arizona, 1547, as a technician named Niman kills a scientist. After a shootout, he flees into the Tunnel. Niman is a spy who has planted a nuclear device in the complex. The guys need to find Niman to get him to reveal the location of the bomb. They lure him in with a fire but he slips, and the Project transfer Doug and Tony after him to 1,000,000 A.D. Niman is already there and has established himself with the ruling clique. The guys get the info on the detonation time, bypass a force field, and with the aid of a local female ""defective"" manage to get to Niman. The Project transfers everyone, including two of the future-types, back to 1,000,000 B.C. After some running around from dinosaurs, they rescue Niman from a quicksand pit in return for the location of the bomb. The head alien eventually comes around and forces Niman to give the location of the bomb which they defuse. Everyone ends up in a giant bee hive and the Project gets everyone but Niman out.

The guys arrive in a brick basement on the North Atlantic coast in 1978. It has advanced electrical equipment, and they are attacked by an overalled man. He collapses dead, then gets up and disappears in a cloud of smoke. They go upstairs and are paralyzed by an alien-android disguised as an old woman. The aliens are preparing to steal Earth's oxygen. The Project staff execute a lateral transfer and free the guys. They escape to a seemingly empty town surrounded by a force field and filled with paralyzed townspeople. A young couple, Paul and Joan, find the guys and tell them about the oxygen-stealing plot. Meanwhile the alien androids infiltrate the Project base, seal it off, and start sucking out the oxygen through the Tunnel itself. The guys must destroy the operation at their end. They fight off the androids and use explosives to blow up the alien HQ.