Red vs. Blue centers on the Red and Blue Teams, two groups of soldiers engaged in a civil war. Each team occupies a small base in a box canyon known as Blood Gulch. According to Simmons (Gustavo Sorola), one of the Red Team soldiers, each team's base exists only in response to the other team's base. Although both teams generally dislike each other and have standing orders to defeat their opponents and capture their flag, neither team's soldiers are usually motivated to fight each other- if they are otherwise, neither are efficient. Teammates have an array of eccentric personalities and often create more problems for each other than for their enemies.
Sarge attempts to intimidate the Blues by announcing the Red's imminent attack. Grif reasons that killing Caboose would remove the point of waging war, as the Blue base has not received any reinforcements, and may never receive any. Sarge reconsiders the attack and contacts Command to ask for advice on dealing with the Blues. Meanwhile Grif confides in Simmons that he would rather stall the battle for years, and be facing one "shitty" enemy, than transferred to a new base and fighting five "real" enemies. Command brushes Sarge off, claiming not to know anything about a Blue team. Simmons recalls that the Reds had deleted the information on the Blues while at Command.
At Blue Base, Caboose appears to talk to Epsilon about his adventures in Blood Gulch with Sheila. Sarge is looking for Simmons so he can brief Red Team on his latest plan to wipe out the Blues. Sarge finds Simmons in the holographic projection room beneath their base, and interrupts Simmons' heartfelt talk with a holographic version of Sarge. Above ground, Grif, Sarge, and Simmons discuss their strategy for combating Blue Team, which involves restoring the information of the Blue Team in Command's databases that was previously erased by Simmons, because the team reasons that they can't beat an enemy that doesn't exist anymore. Sarge tells Simmons to wake up Donut, who was shown to be still unconscious earlier in the chapter, but they find him missing. Once again at Blue Base, Caboose appears to be recounting previous adventures to Epsilon. The camera pulls back and Donut is revealed to be standing behind Caboose.
The Reds are out looking for Donut, heading over to Blue base. Donut confronts Caboose and tells him that he has an important message for Church from Tucker. Caboose quickly explains Church's true nature as an AI and Donut tells Caboose the message instead, saying only that Tucker needs help, and that "it is under the sand" before passing out. Caboose misunderstands the message, but tells Donut he can rest at Blue Base for as long as he needs to. Meanwhile, Sarge, Grif, and Simmons arrive outside and think that Caboose is torturing Donut. Caboose talks with them and Sarge tries to negotiate Donut's release, but Caboose misunderstands the questions, believing the Reds are offering him treats, and becomes angry when they don't give him any cookies. Simmons also becomes agitated with the situation before leaving to "go sleep under a tree until it's over". Caboose goes back inside the base where Donut has regained consciousness. The episode ends with Donut puzzling over the fact that the normally insubordinate Grif is working with Sarge and that Simmons has uncharacteristically abandoned them.
Donut tells Caboose about what happened to him after he was relocated from Blood Gulch, including his debriefing by the Counsellor of Project Freelancer. Donut had arrived at his new base and found a distress signal from Tucker telling him to find Church. Caboose, after explaining the events of Reconstruction to Donut and deciding they need help, calls Washington, who is revealed to be alive but in a maximum security prison. Washington is surprised to hear that Caboose and the Red Team received new bases while he was arrested. He tells the guard he needs to talk to the commander because he just figured out the last part of the "puzzle".
After Washington hangs up on Caboose, Donut offers to help him with his project and mentions that the Red team's underground holo-room could be useful before returning to Red base. After another accidental fire, Caboose decides to take Donut's advice and sneaks off toward Red base with Epsilon, planning to check out the holo-room. There, the Reds are making plans to rescue Donut, who returns and explains his brief visit to Sarge. Only Grif notices Caboose's attempt to stealthily enter Red base, but he ignores him and Caboose gains entry to the holo-chamber. Once inside, Epsilon begins to make humming sounds, which alarms Caboose. The scene fades to black and the chapter ends with Caboose mysteriously exclaiming, "It's you."
Epsilon's storage unit suddenly opens up, and the figure of Delta is seen. He explains that Epsilon chose this form because Delta was the main source of information from Caboose's stories. Delta asks Caboose for his help on a mission; specifically, he asks Caboose to take him to the source of energy that Donut had previously mentioned, and also where Tucker is supposed to be, so they can punish those who harmed Alpha. Delta states that they must find it themselves because Washington doesn't trust Epsilon and Caboose constantly fails at building a new body for Epsilon, explicitly remembering the fires. Caboose agrees to go on this mission. As Delta disappears, the Reds arrive and Caboose tells them that he is leaving to get Tucker. Grif volunteers to go with him so that he can ensure Command acknowledges the Blues exist. Sarge decides to go as well, but Simmons chooses to stay behind with Donut and offer 'logistical support'.
Outside the Red Base the team of Caboose, Sarge, and Grif prepare to leave for Donut's given coordinates while Grif questions the capabilities of their new jeep. After they leave, Simmons informs Donut and Lopez that he is going to blow up Blue Base. After he is gone for a long while, Donut decides to go check on him. Meanwhile, after stopping at a number of bathroom breaks for Caboose, the team arrives in the desert, only to be told to vacate over an intercom. This follows with a warning that they've driven into a mine field. The scene cuts out while Caboose and Sarge question whether or not you can own a field and Grif says that he means explosives, just as an explosion is heard.
Back at Blue Base, Simmons discusses the mess Caboose has made in his project to build a new body, and mentions how nobody has won the war because they waste their time building “stupid robots”, a comment which Lopez takes offense to. Because Lopez is the only one with access to the Red's armory, Simmons tries asking him for explosives, but Lopez deliberately stonewalls him. Meanwhile the voice over the intercom tells Grif, Caboose, and Sarge to remain still so they can work out a way to navigate out of the mine field. After they prove incapable of following simple directions, a frustrated Grif decides to just drive his way out. Explosions are heard off screen while the stranger over the intercom agrees that running is just the best option.
Grif crashes the jeep into the vehicle driven by the person who was trying to guide them out. As Sarge berates Grif, it is revealed that Caboose was blown up by a mine and seemingly killed, but he shortly falls from the sky, perfectly fine. The guide explains that the area is a restricted dig-site, and is soon joined by a friendly alien, "Smith", apparently of the same species as the previous Aliens they'd met, revealing to the surprised soldiers that they are working together. In the meantime, Simmons tries to apologize to Lopez, but again offends him by making a comment about Mexicans holding grudges. Realizing he has blown it, Simmons looks for another way to blow up Blue Base. Elsewhere, Washington is led by the prison guard to a door, and is told he has five minutes to talk with the "man in charge". The door is opened, and the voice of the Chairman is heard off-screen, greeting Washington, saying that they have "much to discuss".
Shortly after Simmons asks Lopez for explosives, Donut comes back from investigating Blue Base for parts, mentioning off-hand that Caboose took Epsilon with him. Simmons becomes upset, as returning Epsilon to the authorities was part of the deal that got the teams their new bases, and attempts to radio Sarge to let him know. Unfortunately, he is unable to make contact as Sarge's radio isn't working. Back in the desert, the guide explains the treaty between humans and aliens and that another human team might cause an incident. He does permit Sarge, Grif and Caboose to scavenge for parts and supplies as long as they don't wander off. As Sarge notes that something "doesn't feel right", the guide tells Smith to return to getting into the temple while he takes care of the others, as the camera swings around to reveal the dead bodies of the real investigation team.
While Grif and Sarge scavenge various jeeps for parts, Grif notes that all of the radios are either broken or have been completely ripped out, preventing them from calling Simmons. When Caboose suggests he can "fix" one of the missing jeep radios, Grif decides it best not to reason with him. While Sarge and Grif discuss the strange situation, Grif realizes that the investigation team's mobile base probably has a radio. Just then Epsilon's distinct sounds can be heard. Grif startles Caboose and he drops Epsilon’s carrying unit, just as the man from before approaches from the distance. Meanwhile, at Red Base, Lopez has assembled two motorcycles in order to allow Simmons and Donut to find Sarge, or so Simmons thinks. Lopez reveals that after years of working with the Red Team he builds two of everything, and sure enough Simmons destroys one of them immediately as he goes to retrieve Donut from Blue Base. Back in the desert, the man introduces himself simply as CT. CT notices Caboose is gone and points a gun at Grif, demanding to know where Caboose is, a threat with which Sarge has no problem. Just then an alarm sounds and various other soldiers and aliens are seen running towards the mobile base, while Grif confirms that it’s probably Caboose’s doing. CT orders Sarge and Grif to move in the same direction.
Caboose's sneaky antics have aroused suspicion among the Desert dig team.
Tucker attempts to explain the situation to the Reds.
Simmons and Lopez try to hold their ground, while the desert team members find themselves in shifting sands.
Epsilon Church takes charge of the escalating situation at Sandtrap, while the reds back at Valhalla have their hands full.
Church is having a little trouble with the "out of the box" experience.
Things start to shake up on Sandtrap, while the Reds at Valhalla spring into action.
Church learns that with great power, comes great responsibility... also a wicked left hook.