In the first episode of season 3, the Reds and Blues find themselves scattered across the universe as they attempt to hunt down evil mastermind O'Malley.

Sarge and Caboose try to escape from a bizarre battle between two groups of unknown Red and Blue soldiers.

O'Malley sets his evil plans in motion, while the Reds and Blues debate their next move.

Church and Grif get used to life on the inside, while Simmons and Donut attempt to reprogram the teleporters.

The Reds and Blues must work together to stop O'Malley and disable the ten megaton bomb inside Church's body.

Grif and Simmons try to make sense of their new futuristic surroundings, while Caboose helps Donut with an important discovery.

Sarge and Donut attempt to fix the Warthog while O'Malley and Lopez inspect their new home.

(Episode 45.9) Available only to sponsors or on the Season 3 DVD and produced solely by Gustavo Sorola while the rest of the production crew had been out of town. This episode continues or replaces the events of episode 45, though is non-canon, and features paper cutouts as characters while portraying Simmons as a hero.

O'Malley and Lopez receive an unexpected visitor, and the Reds intercept a transmission from an old adversary.

The Reds and Blues meet up with Tex and plot ways to infiltrate O'Malley's compound.

Sarge and Tex lead an offensive against O’Malley, with Caboose doing some heavy lifting.

Church seeks help from an ancient computer, while the Reds search for the missing head of Lopez.

The computer completes the teleporter and reveals its name to be Gary. Church teleports back to Blood Gulch shortly before the series begins. Another Church runs in and tells Gary to teleport him to Sidewinder instead, because he "screwed everything up." On Blood Gulch Church finds that he either has no effect, or causes the previous events by his presence.

Church discovers the event of the past are hard to change, and even harder to believe.

Church’s travels through time lead him into an unexpected temporal loop of confusion.

Tucker shows off his new bling while the Reds monkey about.

The Reds debate the source of an incoming distress signal while Caboose introduces everyone to his new friend.

Church tries to placate Andy, and Grif gets the wrong idea.

O’Malley and Lopez begin their attack… their very, very slow attack.

Church tries to figure out the prophecy of the “Great Destroyer” as O’Malley’s Robot Army inches closer.