Tony and Doug arrive outside the tent of Joshua on the sixth day of his seven-day assault on Jericho. With their future knowledge of the Bible they are able to convince Joshua that they are emissaries of the Lord, and he basically forces them to go into Jericho as spies. Doug is captured and tortured after they try to stop an exection, and Tony befriends a harlot, Rahab. With the help of Rahab and her father, a blind architect, they manage to free Doug. Tony and Rahab are set up for execution, but when a skeptical Anne tries to use the Tunnel to free them in opposition to how the Bible describes the incident, the Tunnel shuts down as if by some outside (dare we say Divine?) force. Tony and Rahab are spared when Joshua launches his attack and both the guys and the Project team witness the miracle just before they are whisked away once more.

Doug and Tony arrive in Lincoln in late April in the 1860s, and run afoul of Billy the Kid. Doug shoots Billy and apparently kills him, then he and Tony escapes. It turns out Billy took the bullet in the belt buckle, and he goes after the two. They manage to capture him thanks to a voice-transmitted distraction provided by Kirk, but Tony goes back into town and is mistaken for Billy. Pat Garrett arrives and eventually convinces the sheriff that Tony isn't Billy, but the mob isn't hearing it. Billy catches up to Doug and challenges him to a gunfight. Pat and Tony get involved, with Tony knocking out one of Billy's men planning to backshoot Doug and Pat intervening when Doug blows it. The two men are whisked off again.

Arriving in Gettysburg in the 1860's, Doug and Tony are separated by an explosion which seemingly gives Tony. A jolt from the Tunnel revives him but with amnesia. Doug falls in with the Union forces, while Tony becomes involved with the South and Sgt. Maddox when he is mistaken as a courier sent to buy gunpowder from an arms merchant, Michaels, who stole the stuff from the Union. Doug gets there first to find the merchant is Machiavelli! Apparently Machiavelli's pattern matches Tony's, and he was swept up and brought to Gettysburg by the Time Tunnel. The Tunnel send Machiavelli's dog back when it's about to kill Doug, draining them of power.

The amnesiac Tony takes Doug prisoner and turns him over to his sergeant, while Machiavelli delights in the carnage. Doug escapes and tries to save Tony who is determined to complete his mission. Machiavelli kills Maddox and then Doug and Tony fight when Doug tries to destroy the gunpowder. The two men come to terms but when Machiavelli tries to de

Tony and Doug arrive in Khartoum, November 2, 1883, in the middle of a battle between British and Arab forces. However, two aliens take them prisoner. The aliens plan to conquer Earth with missiles, and will be ready to launch in two hours - they send a bomb to the Project to prevent them from interfering. Tony is taken to be killed but the alien with him is forced to teleport out when the British approach. Then both guys are transferred out of the cave by the Tunnel staff, where they make contact with Captain Henderson and convince him about the aliens. The three of them attack the cave and manage to stop the aliens, with some help when the Project send the bomb back to the aliens.