Church returns to the Blue Base where Junior, the baby to which a now-comatose Tucker has given birth, is wreaking havoc off-screen. Church and Doc argue about the child until a spaceship crashes into the gulch on top of Donut; Church leaves to investigate. The Reds bicker about rescue plans until Sarge leaves to fetch a rescue device. Church arrives and claims the ship with Sheila's support.

As Church argues with Simmons and Grif, a tapping noise begins to sound from the ship. Sheila abruptly leaves, forcing Church to retreat to the base.

Church attempts to call Vic for reinforcements, but is stalled by an elaborate answering machine system. Meanwhile, the back door of the ship opens, and an unseen entity emerges.

Church finally discovers that Vic's voice mailbox is full. The Red reinforcement who emerged from the ship is revealed to be the Sister of Grif, who by Simmons' theory arrived using the ship's light drive, which caused her and the ship to move forward in time as it was traveling to Blood Gulch. Meanwhile, it is revealed that Donut fell into an underground cave (Waterworks in Halo 2) after the ship crashed on top of him.

As Caboose attempts to see the new Red soldier using the sniper rifle, Church speculates as to what combat skills the reinforcement may have. Tucker wakes from his coma and joins them, immediately identifying the new soldier as a girl from hundreds of feet away. Sister explains to the Reds that, following the death of a Team Commander, Command has promoted a soldier to the position and sent her to fill the new low-level opening. Since Command seems to presume him dead, the Reds decide to hold an impromptu funeral for Sarge.

The Red Team holds Sarge's funeral, each giving a separate eulogy. Grif makes jokes; Simmons announces his campaign for Red leader; and Sister goes on a tangent about death and age. Finally Sarge, disgruntled, is buried alive.

The Reds argue whether to keep Sister, before Grif secretly decides to rid the team of her before the still-buried Sarge discovers her Blue allegiance. Doc examines Sheila for her random behavior since abandoning Church in episode 79. Grif confronts the Blues and convinces them to take Sister. Simmons appears after trying to dig up Sarge, and proclaims him missing.

Church gives Sister an orientation, before Tex arrives. Meanwhile, Simmons explains that he discovered a large cavern under Sarge's grave.

Grif and Simmons decide to enter the cave. Meanwhile, Tex is firing at the Blues to try and deduce who is being possessed by O'Malley. Church starts to suspect that Sheila is possessed by O'Malley, causing her malfunction. Tex notices Sister, and reacts jealously.

Soon after Sarge awakens underground, Donut discovers him. As Tex and Sister talk, Church and Tucker discuss having two girls at the base. Back in the cavern, Donut points out what he believes to be a subterranean Blue base, the two bodies he found earlier, and a vehicle resembling the "motorcycle" he stole from O'Malley. Simmons and Grif reestablish radio contact with Sarge, and decide to meet.

Simmons and Grif are shot with projectiles which resemble tranquilizers in effect while waiting for Sarge and Donut. The Blues decide to reboot Sheila.

Doc decides to give Sister a physical. Donut and Sarge find a briefly unconscious Simmons who explains that his attackers have apparently taken Grif with them. At first reluctant, Sarge decides to go help find Grif after realizing his prized shotgun was taken too. Using a tracking device in Grif's armor, they discover he is about a tenth of a mile away and head to find him. The Blues decide Caboose will distract Sheila while Tex shuts her down.

Tucker and Junior overhear Doc's inspection of Sister. Meanwhile, the Reds find Grif, who claims that he was questioned by his captors. As the Blues reboot Sheila, the tank shuts down just before revealing O'Malley's new host to Caboose.

The Blues decide to transfer Sheila's intelligence to the crashed ship's on-board computer. Grif recounts his interrogation, and how Andy was present and translating for his captors, who are looking for "the kid and the sword".

Tex recounts the events of Red vs. Blue: Out of Mind. When York's presence in the future is questioned, Tex comments that, as part of her division's AI implantation process, his armor's special healing ability might have kept him alive. When it is revealed Wyoming teleported away from her before she could question him, Church remembers Gary's ability to create teleporters, and decides he must be Wyoming's AI, Gamma. Church is then called by Vic and told to attack the Reds via the caves. Meanwhile, the Red team discover a surveillance system watching over Blood Gulch in the cavern.

Church somewhat follows Vic's instructions by sending Doc, Sister and Junior through the caves while Church, Tex and Tucker attack the Red base head on. Tucker gives some unhelpful life advice to Junior before heading off. Caboose stays at the base to ensure Sheila's transfer is not disrupted.

The Reds see the Blues advancing on their base on the surveillance system, prompting them to find their way out of the cavern to invade the deserted Blue base. Caboose asks Sheila, now uploaded into the ship, where O'Malley is, relaying Tex the answer. Tex then confronts Church, calling him "O'Malley." Doc and Sister head through the caves, where they find Lopez's disembodied head.

Sarge calls Command for reinforcements, and Simmons hears an echo and leaves to investigate. He traces Vic Jr.'s voice back to the surveillance monitors, and as Simmons' voice is heard, he quickly hangs up on Sarge; the Reds assume the equipment is interfering with their radio signals. Meanwhile, Caboose explains that Sheila said O'Malley was inside the "Blue Leader." Church protests that he was never officially promoted to that position, and is not O'Malley's host. In the caves, Doc, Sister and Junior are approached by a new Alien and his partner, a revived Captain Butch Flowers, now host to O'Malley.

The Blues at Red base are ambushed by Wyoming, and Church attempts to secretly call Caboose for help, but he fails to understand. The tank nevertheless leaves for the Red base, unmanned. The Reds find Andy in the caves, who explains that the New Alien revived Captain Flowers, and begins to explain why O'Malley and Wyoming want Junior before the Reds cut him off by leaving. Tex engages her camouflage to escape Wyoming, and the tank arrives, but is revealed to be controlled by Gary.

Caboose deduces that he must leave Sheila to help his teammates at Red base. Meanwhile, Tucker finds out that Wyoming has the ability to loop time, having gained it from the AI implantation process, just like Tex's camouflage and York's regeneration. By rewinding events until he is victorious in battle, Wyoming is able to detect the invisible Tex before she attacks and kill Caboose. Tucker uses his knowledge of the loop to impale Wyoming with the sword, and save his teammates. When told of the loop, Church wonders if copies of Wyoming were made, as they were when he time-traveled, when the two come across multiple Wyomings.

Flowers/O'Malley and the New Alien are revealed to be holding Doc, Sister and Junior hostage at the underground surveillance system; Flowers mentions to Vic Jr. the plan to give Junior the sword in order to grant him unstoppable power, and that the New Alien is oblivious to their plan. Meanwhile, Church and Tucker manage to escape most of the Wyomings as the time loops continue, which Tucker states that he is aware of because of his possession of the sword, according to Wyoming. Gary is disabled after Tucker connects him to Sheila, and she traps the enemy AI behind a firewall, halting the time loops and the production of new Wyomings. The Reds decide to enter the battle in the Warthog (complete with the classic Tejano music), and take out all of the Wyomings but one. The plan is then revealed: Junior is to become the ruler of the alien race, and O'Malley plans to infect him to exploit their entire civilization in order to "win the war at any cost." Wyoming says that Tex will aid them now that she knows of the plan, and to Church's disbelief, she announces herself on an open radio channel, taunting O'Malley to "come and get her."

Official Ending - Tex reasons that ruling the Aliens would win the war. Church, arguing O'Malley can't be trusted in a deal, begins broadcasting on an open channel to prevent O'Malley from jumping into Tex. As Tex kills the last remaining Wyoming, O'Malley accidentally infects Simmons. Tex knocks Simmons out, and follows O'Malley into Caboose's mind. Church approaches the Reds and warns them to disable the ship so that O'Malley can't escape, before entering Caboose as well.

Inside Caboose's mind, Church finds Tex and O'Malley negotiating their deal to rule the Aliens. He kills them both, causing them to leave Caboose's mind. After killing himself, Church emerges from Caboose's head to find that in the interim Tex has taken the sword, while Junior and the New Alien have boarded the ship.

O'Malley then infects Donut. Tex then knocks him out forcing O'Malley to jump to a different host. After jumping to multiple hosts, O'Malley jumps back into Tex and boards the ship to escape. However, Sarge has placed Andy on board, and gives the order to detonate. The ship disappears, followed soon by an explosion.

Official Ending - Alarm

The Blues retreat to their base. Some time later, the teams loosely echo each other's episode 1 dialog, before Sarge calls the Reds to name a new ATV he built.