The first episode of Red vs. Blue introduces the main characters, and poses the all-important question, why are we here?

The Reds get a new piece of equipment, and Grif has a problem with its name.

The Red and Blue armies get new recruits.

Caboose is given the job of "guarding the flag". Donut goes to the store.

Donut returns from the store with a surprise.

The Blues go through the teleporter. The Reds get the upper hand.

While Church and Tucker lament their current situation, Caboose hops into the tank.

Grif and Simmons flee as Caboose's trigger happy firing has dire consequences.

The cavalry arrives, and Caboose gets stuck.

Tucker requests reinforcements, and gets more than he bargained for.

Tex assaults the Red Base, injuring donut and knocking out Grif and Simmons.

Church reveals that Tex was his former girlfriend and the Red Team airlifts a severely injured Donut back to headquarters.

Simmons and Grif guard Tex while Church explains to the Blues about Tex's AI.

The Blues fake an attack on the Reds in order to free Tex and inadvertently get Sarge shot in the head.

Sarge and Church meet up in the spirit world and talk about the afterlife until Sarge is revived by Grif.

Donut returns with new armor, and Lopez finally speaks.

The origin points here.

Church tries to warn the Red Team of Tex's impending attack.

The final episode of Red vs. Blue season one.

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.

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.

Medical Officer DuFresne (Doc) arrives at Valhalla after Simmons had requested a medic from Command. Doc is initially happy to meet Simmons again, but Simmons says that Donut needs his help. Doc notes that Donut is dead, and that nothing can be done for him. Simmons says he is sorry, and admits that he sent the request because "they" forced him to, needing someone with medical training. Doc turns around to see Washington and The Meta, who knocks him unconscious. In the desert, Epsilon Church is enjoying his new status, making up speeches while being worshiped as a deity by the aliens. While delivering a eulogy for C.T. and the human members of his team, Epsilon Church trails off when he sees a dark figure in the distance. He follows the figure; as it walks into a building, he finds himself at the Valhalla installation. When Tucker gets his attention, Epsilon Church again finds himself back in the desert. Realizing that Epsilon Church has just had another flash of memory, Tucker tells the Reds that this has been happening with increasing frequency. When Epsilon Church recalls seeing a waterfall, Grif and Caboose say that it sounds like the Valhalla bases.

As Sarge makes preparations to call Simmons to get his take on Epsilon Church's visions, Doc recovers and wakes up at the base with Simmons, who explains the details of Washington and the Meta to him. After hearing that Doc had experience with Omega previously, Washington tells him to examine the Meta, who is suffering from armor problems. Back in the desert, Sarge uses Epsilon Church to boost the Warthog's radio and contacts Simmons, but receives a forced message from him under Washington's supervision. Fortunately, using nothing more than his knowledge of his teammates and Simmons' communication, Sarge instantly deduces the situation at Valhalla. As he and Grif set off to rescue them, an intrigued Epsilon Church follows.

Doc informs Washington that the Meta is physically healthy, although having serious problems with his armor. In the desert, Tucker searches for the Reds and Epsilon Church, and guesses they must have taken off. Caboose warns Tucker not to say anything about Epsilon Church missing, as the aliens would become hostile if they knew he was gone. Meanwhile, Sarge arrives in Valhalla to help out Simmons and Doc, and attempts to lure Washington to the center of the canyon. Washington moves to out to intercept him after telling The Meta to kill the prisoners if Sarge caused him any problems. With Washington gone and the Meta distracted, Simmons and Doc plan to short circuit the Meta's suit using an overpowered charge on Doc's medical scanner. Washington confronts and disarms Sarge and demands to know where Epsilon is, but at Sarge's signal, Grif bursts through the canyon wall in the Warthog, landing on Washington and pinning him under the car. With the Warthog still moving at a high speed, Wash climbs from under the Warthog and onto the front, and attempts to shoot Grif. Grif slams on the brakes and Wash is thrown into the opposite cliff alongside explosive barrels as Sarge reclaims his shotgun. He fires at the barrels to ignite them, attempting (but failing) a one-liner, and Washington is engulfed in the resulting explosion. As the episode ends, the Meta sees the explosion and readies to execute Doc just as Doc charges his "scanner."

Epsilon-Church finds the gap in the Valhalla wall caused by the warthog, and continues to follow the reds. At the base, Doc fires his medical scanner at the last second, blasting the Meta against the wall. The blast overloads the Meta's temporal distortion unit, causing him to be slowed down rather than him slowing down time. However, he is still able to land a single punch that caused Doc to fly back and get trapped in the wall. As Sarge and Grif arrive, Simmons declines to help Doc as the Meta begins to resume normal speed, and rejoins his team. Returning to normal temporal relativity, the Meta pursues the fleeing red team, destroying their warthog. As the reds prepare to make a last stand against the Meta, Epsilon-Church arrives, serving as a decoy to lead the Meta back towards blue base while the reds escape. Red team runs back through the hole made by the warthog, arriving in Isolation. As they catch up, Epsilon-Church appears and reveals that he lost the Meta, but is still being followed. He is about to reveal who he came here to look for, the reds begin insulting him, so that he may activate his laser and seal the gap, preventing the Meta from pursuing. It doesn't work at first, but when the Meta and the now-recovered Agent Washington appear beyond the hole, the sight of Wash enrages Epsilon-Church, who inadvertently fires his energy weapon and seals the gap, trapping Wash and the Meta on the other side. This frustrates Epsilon-Church, but before he says why, he loses power and falls. Back in Valhalla, the Meta is angry that they got away, but Washington mentions that they still have a source of information: Doc, who is still trapped in the wall at blue base.