Donut tries to coax an injured Tucker into getting up, conveniently providing a recap of the end of the previous season in the process. Sarge and Caboose find themselves in Battle Creek, in the midst of perpetually respawning Red and Blue soldiers ("Grunts"), who engage in a complex action sequence that lampoons multiplayer game sessions in Halo. Meanwhile, Simmons is lost in a place full of teleporters (the Chiron TL34 map), and Grif and Church have been imprisoned by the Red Team on Sidewinder.

In an unknown location, Wyoming, another freelancer, interrogates a soldier named Phil, but is interrupted by a phone call hiring him for another job. Meanwhile, still in Battle Creek, Sarge and Caboose steal the Red and Blue flags in an attempt to coerce the teams to help them find their way out. When that fails, Caboose recalls O'Malley's possession, unleashes his angry side, and single-handedly eliminates both teams. Simmons then retrieves them via a teleporter.

O'Malley calls Vic and reveals his plot to eliminate both the Red and Blue Teams and to rule the universe. He also informs Vic that, to preserve Vic's secret, he has hired an assassin to kill Tucker, the only person who knows that Blue Command and Red Command are the same. Back in Blood Gulch, Tex tells Tucker that Wyoming, the assassin hired to kill him, is a freelancer from the same experimental program as Tex, and, like Tex, he had been enhanced with artificial intelligence. Still in the teleporter hub with Simmons and Caboose, Sarge contacts Donut to inform him of the "Blue plot" and that Tucker's idea that Red and Blue are the same is nothing but a deception. Wanting to help to find Church, Caboose unwittingly presses a button that activates the bomb in Church's robot body. On Sidewinder, Church consequently lets out a large belch, and his stomach begins to tick.

Simmons reprograms a teleporter and advises Donut on how to reprogram the Reds' teleporter in Blood Gulch. On Sidewinder, Wyoming kills all of the Reds and tells Church and Grif that he is leaving them to starve to death. Meanwhile, everyone else emerges from the teleporter on Sidewinder, Tucker covered with "black stuff" (which luckily prevents Wyoming from recognizing and shooting him). While Donut and Caboose clean off Tucker's armor, the jail cell holding Church and Grif mysteriously opens. Wyoming spots Tucker from afar and aims at him; Tex ambushes him, but O'Malley, Wyoming's employer, ambushes her.

O'Malley activates Lopez's "secret weapon", a weather control device that Sarge had almost finished. The Red and Blue Teams join forces to confront O'Malley, who begins to wreak havoc with his rocket launcher. Simmons manages to teleport the Battle Creek players to Sidewinder and convinces them to attack and defeat O'Malley. Lightning from Lopez's weather device hits Church, thereby damaging the bomb in his body. When Sarge is subsequently unable to disable the bomb, Tucker tries to destroy Church with O'Malley's rocket launcher before Church explodes, but Wyoming snipes the launcher out of Tucker's hand. The bomb explodes and, due to the damage received from the lightning, destroys the present as well, sending both teams (except Church) to the future (Halo 2). Donut attempts to direct a play to explain this sequence of events to Tucker. The group reasons that they were blown into the future because they were standing in front of Church; Tucker deduces that Church must have been blown into the past. Meanwhile, on a Marathon 2 map, Church appears, wondering what has happened.

Exploring the wasteland in the future, Grif, Simmons, and Tucker discuss various Hollywood post-apocalyptic clichés. The group finds a jeep and bickers over it. Tucker is bent on finding Church, but Sarge asserts that Church, along with the group's enemies, had died in the explosion. Meanwhile, a cackling O'Malley discovers Lopez's disembodied head on a beach.

While Sarge and Donut try to repair the Warthog, Grif, Tucker, and Simmons argue about styling the jeep in order to attract women. Tucker still maintains that Red and Blue are the same, but no one believes him. Meanwhile, O'Malley, Doc, and Lopez inspect some real estate (Zanzibar in Halo 2); O'Malley and Doc argue over its viability and over how the computer inside should be used. This episode marks the final appearance of the weapon reticle in footage filmed with Halo 2; going forward, the Rooster Teeth team has exploited a gameplay bug to remove it.

(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.

Having moved into the fortress, O'Malley, Doc, and Lopez repair the turret emplacements and meet The Red Zealot, who believes that he has found a holy temple. Exploiting the Red Zealot's religious fervor, O'Malley deceives him into performing menial tasks for him. O'Malley then catches a glimpse of Tex, who is spying on him, but on subsequent glances, sees nothing. Elsewhere, Sarge, Grif, and Simmons discuss the results of Grif and Simmons' failed reconnaissance, and, while attempting to push the Warthog out of a ditch, receive a transmission from Tex informing them of O'Malley's location.

The Reds, Tucker, and Caboose meet with Tex on the beach near O'Malley's fortress, where she reveals her plan to destroy both O'Malley and the entire base by planting a bomb inside. Tex has scouted the base and found the exact location to place the bomb. However, citing the bomb's immense weight, she has someone else carry it; of the others, only Caboose can lift it. Meanwhile, the Red Zealot informs O'Malley and Lopez that a crowd of people is gathering on the beach. Upon learning that Lopez is inside with O'Malley, the Reds balk at destroying the base, but Tex refuses to risk losing her chance to defeat O'Malley. Tucker solves the problem by reminding the Reds that, since Tex is a mercenary, they can simply hire her to help them to retrieve Lopez. Tex agrees to this arrangement for a future favor.

After discarding two of Sarge's suicidal battle plans, the Blood Gulch group invades O'Malley's fortress and are pinned down by mini-gun turrets manned by the Red Zealot and Lopez's head. Tex snipes Lopez's head off his turret, but the Zealot pins her down with gunfire. Simmons and Grif manage to enter the base and move on to look for O'Malley. Tucker, who had fallen into a hole near the windmill, finds a mysterious sword, and uses it to kill the Red Zealot. Meanwhile, carrying the bomb inside the fortress, Caboose mistakes Tex's "X" marking for a plus sign. He continues on and stumbles across a computer, from which he hears the voice of Church.

In the past, Church (as a Marathon character) finds a computer terminal, which answers some questions for him. Church is in the housing facility for The Great Weapon, which The Great Destroyer will use to bring Great Doom to the galaxy in 1,856 years. When computer describes The Great Destroyer as a "blue being" who "will be known as the stupidest life form in the universe", Church assumes that it must be referring to Caboose. 1,856 years in the future, Caboose asks Sarge to look at the computer terminal, which is playing a message from Church. The message tells Caboose not to touch anything, lest he bring about Great Doom. Specifically, Caboose should avoid bringing the "glowing sword weapon thingy" into the base, as the place will lock its doors. Tucker and Donut stroll in with the sword, and the base locks down, with Caboose's bomb already counting down inside it. In the past, Church finishes recording his message, but, deciding that it will not suffice, asks the terminal to transport him to Blood Gulch so that he can prevent the whole fiasco. While telling jokes to pass the time, the terminal begins the millennium-long process of researching and building a teleporter.

The computer completes the teleporter and reveals its name to be Gary. Church teleports back to Blood Gulch shortly before the series begins. The moment Church is teleported away, however, another Church runs in and tells Gary to teleport him to Sidewinder instead, because he screwed everything up. Back at Blood Gulch prior to the events of episode 1, this Future Church decides to try and prevent the death of Tex, which would prevent O'Malley from escaping and causing the events leading up to The Great Doom. He finds, however, that he either has no effect, or causes the events by his presence in the first place: * Lopez's legs malfunction because Future Church, in trying to get him a larger switch, kicked dirt into the switch Sarge decided to use when building the robot. * Prior to episode 1, the Blues were under the charge of Captain Butch Flowers. Knowing Flowers would die, Future Church gives him aspirin, but Flowers dies of a heart attack due to an allergy of the medicine. Tucker, at this point in Blue armor, takes Flowers' cyan armor. * Donut, in rookie Red armor, finds the Blue Base and steals the flag because Future Church, failing to recognize him outside of pink armor, gives him directions. * Future Church attempts to prevent the death of his past self, which would stop Tex from arriving in Blood Gulch. He awakens the tank and runs through her protocols to try and prevent her from shooting him later. She refers to herself as Phyllis, and overrides her name when Church addresses her as Sheila. Future Church turns off a "friendly fire protocol," which in actuality prevents friendly fire; thus the original Church's death takes place because of Future Church. * Finding a sniper rifle on the corpse of his past self, Future Church picks it up but drops it later. Caboose finds it, and uses it to shoot Sarge. * Attempting to kill Donut to stop him from killing Tex, Future Church fails and retreats to the cave, frustrated. Caboose spots what "looks like Church," and turns on his radio. As a result, O'Malley infects him.

The funeral of Church and Tex, prior to the events of Season 2, takes place. Future Church continues his attempts to change things for the better, but still ends up causing the disasters he was trying to prevent: * Future Church, posing as Captain Flowers, contacts Vic to try and get him to tell the Reds to get rid of Doc, to stop the medic from being infected by O'Malley. Vic misconstrues his words to believe the Red and Blue teams have merged, but that the soldiers must not know. Thus, the Red and Blue Commands merge. * To stop them from making a robot army, Future Church tries to dissuade Lopez and Sheila from the idea. Instead, he gives them the idea himself, and they decide to build and hide a rocket-launching vehicle in the caves. * Future Church decides to fix the Red teleporter before it malfunctions and sends the characters to various places, just as Sheila rams the base. Future Church is knocked out, and the teleporter begins giving off sparks. * During the Mexican standoff where O'Malley appears, Future Church finds a rocket launcher and aims to take the villain out. Instead, he shoots and injures Tucker from behind, and again decides to retreat to the caves.

Future Church watches Tex, Donut and Tucker leave for Sidewinder, and soon follows them. He talks first to Sheila before leaving for Sidewinder, asking her to do him an inaudible favor. Once at Sidewinder, Future Church finds his past self and Grif in prison, and opens their cell by pressing a button in another room. He attempts to contact Tex, who is currently being held by O'Malley and Wyoming, before another Church approaches him. This new Church claims that he fails to stop the bomb, and gets blown back in time again, only to return to Sidewinder. He then tells Future Church to "meet us at the top of the ramp." The bomb goes off, and Future Church is sent back in time. As seen in Episode 50, as soon as Church is teleported by Gary to Blood Gulch, Future Church arrives and asks to be sent to Sidewinder because he screwed everything up. Just then, more Churches arrive, each having been unsuccessful to stop the bomb, and thus sent back in time to Gary. These Churches all meet in Sidewinder, and explain to the newest Church how their various plans failed. It is determined that whichever Church did each one of these plans already must be the successful Church, since he isn't sent back in time again. This Church gives up on trying to correct everything, instead freeing Tex, and rejoining the Blood Gulch soldiers before the explosion, thus being sent into the future. Church emerges at O'Malley's base, just in time to ask Gary, who remains there, to stop the bomb from detonating. He then prepares to explain the events he went through.

Caboose asks Church why he did not try to save himself, Tex, or create millions of copies of himself trying to defuse the bomb when he was in the past. Church warns Tucker that Gary said the sword was dangerous, but Tucker blows it off. Meanwhile, the Reds covertly meet to discuss a distress signal on the Red Army's open channel, which was picked by the radio in the Warthog. This episode features an unknown character ducking behind a rock.

The Blues watch the Reds play with their radio, at a loss for a motive. Caboose explains that they are talking about the distress signal, an explanation he got from "Andy". The Reds are discussing the distress signal, which Simmons cannot pinpoint due to the substandard equipment. Caboose introduces Tucker and Tex to "Andy": the deactivated bomb. Predictably, it won't talk to them. However, Gary the terminal knows Andy very well. This episode also features another distant character.

Andy starts talking to the rest of the Blue Team, and is quickly revealed to be rude and volatile. Caboose and the Blues try to calm him down so he won't explode. Meanwhile, the Reds are planning on escaping in the Warthog to find the source of the distress signal. Grif is sent to find out what the Blues are doing, only to be confused when he finds them trying to soothe Andy. Unbeknownst to all, O'Malley has assembled a huge army of robot Lopez duplicates outside the base, which he orders to kill everyone and retrieve the "device".

The Reds puzzle over why the Blues were talking to the bomb, and Sarge concludes that they are trying to re-arm it as part of a pre-emptive attack strategy. O'Malley's army turns out to be extremely slow-moving: Lopez built them that way so they would win in exactly 24 hours, since O'Malley said he wanted a day of victory. Meanwhile, the Blues have finally managed to calm Andy down, but are interrupted by explosions and plasma fire as O'Malley's attack begins. Believing that the Blues are attacking, Sarge orders the Reds into battle.

O'Malley berates Lopez for creating such a slow moving army. In revenge, Lopez tricks O'Malley into insulting himself in Spanish. The Reds flee the battle in the Warthog to track down the distress signal. Donut is left behind to discourage pursuit, but manages to steal O'Malley's hovercraft and rejoin his teammates. Tex steals Tucker's sword so she can fight the robots; Church decides that she must be The Great Destroyer from the prophecy. An unseen figure wipes out O'Malley's army with a volley of plasma grenades, and then attacks a startled O'Malley. Lopez's fate is left unrevealed. Shortly after Donut catches up with the other Reds in a cave, Simmons and Grif track the signal out of the cave, finding themselves back in Blood Gulch (Coagulation in Halo 2). This discovery is accompanied by a lengthy scream of "Noooooooooo!" from Grif. Back at the fortress again, Church and Tucker admire the slaughtered robots and congratulate Tex, but she admits she's not responsible: she was in the basement, trying to get the sword to work. Church rushes over to Gary to question him about the identity of The Great Destroyer, unaware that an Alien is sneaking up on him.