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.

Church discovers a note from Sheila and Lopez confirming that they have started a robot army. At the Red Base, Sarge unveils the two new robots; one contains a microphone to spy on the Blues, and the other contains a bomb. The Reds and the Blues meet in the center of the gulch to execute the exchange. Sheila and Lopez also arrive to conquer the Blues; Lopez becomes angry at seeing new robots brought into the conflict, and rushes forward to attack. A tense Mexican standoff results, and Sarge tries to call an air strike. However, due to crossed communication channels, Tucker intercepts his message, and realizes that Vic is apparently working for both Red and Blue Commands. While Church possesses one of the robots, Tucker tries to alert everyone that Red and Blue are the same, but is hit by a rocket before anyone can understand him. His attacker is apparently Doc, possessed by O'Malley, who flies around on the hovercraft, firing rockets at will. In the ensuing chaos, O'Malley takes Lopez as a hostage, announces his intention to conquer the universe, and disappears through the Red Team's teleporter. The Reds and Blues call a temporary truce to pursue Doc, whom the Blues need to heal Tucker, and to retrieve Lopez, whom the Reds need for the plans his memory contains. Donut, Sheila, Tucker, and one of the robots remain behind in the gulch while everyone else follows through the teleporter. Tex soon surfaces in the remaining robot body. Unfortunately, due to a teleporter malfunction, the pursuing Reds and Blues end up separated and scattered across different places. Simmons ends up in a huge area full of teleporters, Church and Grif end up captured by Max Gain, a member of the Red team in Sidewinder, and Sarge and Caboose appear in the stream in Battle Creek.

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.

Grif and Simmons flee from Caboose and Sheila; Grif abandoning Simmons after he had hatched a plan for a joint escape. Once Caboose manages to activate the auto-fire mechanism, the tank begins to systematically target and destroy everything present. Sheila subsequently hits the Warthog, sending it flying, but Grif and Simmons continue to flee and successfully evade the cannon fire. Church becomes the next target, however, and is killed when Caboose fails to deactivate Shiela's auto-fire operation; Tucker accuses Caboose of team-killing ("You shot Church, you team-killing f***tard!").

The Blood Gulch Crew seek help from Dr. Grey in order to gain more information on the alien temple.

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.

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.

Grif searches for Kimball in the crowded city of Armonia, showing off just how much life has changed on Chorus since the civil war ended.

The Freelancers have done their part. Now it's up to the Reds and Blues to finish it.

The Blue Team discuss which Red soldier they will kill, in order to even the teams. After much pointless discussion, Tex shoots a disguised Lopez, resulting in Lopez's body to be a mere head. Donut, thinking Simmons was the one killed, cries in sorrow after seeing his death. The Blues then decide not to kill any more soldiers. In the Freelancer backstory, Teams A and B begin their missions. Team A enters the 110 story building and York unlocks a door for them. He accidentally, however, activates an alarm, causing two Insurrection soldiers to go look for them. Back at Blood Gulch, The Reds try to make a eulogy for the death of their teammate. Unfortunately, nobody can figure out the right words to say. Simmons, however, walks up to them and is overjoyed that they are talking about him. He tells Sarge to finish his eulogy. However, Sarge says that Simmons was always there for work and talked a lot, much to Simmons' dismay.