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.

The Reds return to the desert to find Caboose being threatened by the aliens as a result of Epsilon-Church going missing. Tucker informs the aliens that the Reds took Epsilon in order to draw them off of his own back. Meanwhile, as Simmons and Grif try to wake up Epsilon-Church, Sarge is leading the aliens, and thanks to a series of warnings, Grif is able to punt Epsilon away just after he comes to. The aliens arrive with Sarge to see no signs of Epsilon-Church. The Reds flee in the midst of the distraction, and Caboose abandons Tucker, leaving him to face the aliens alone. The Reds and Caboose locate Epsilon, who landed in the mine field after he was punted away. Grif tells Simmons, who is unaware of the mine field, to go get him and Simmons hastily retreats when he accidentally activates a mine.

Washington and The Meta plan to interrogate Doc after they pull him out of the wall with an anchor but it does not go as they had planned, meanwhile The Reds and Caboose get visited by a memory of Delta who tells them that Epsilon is not in control but searching for memories as, Epsilons encounter with Washington has jogged many of its memories, and that Epsilon has not "Coped" with the memories well and fears Epsilon will pursue "certain" memories in particular and states that Delta himself and the other memories of the Alpha fragments will not be able to hide much longer as he states Epsilon will be aware of their presence eventually.The Delta fragment warns Caboose that "Memory may be the key, but everything that is locked is not meant to be unlocked" and leaves before he is discovered. Epsilon-Church awakens again and says he remembered something important and that it may be able to help him and asks Caboose to accompany him to a facility before night fall.

Having set the piece of wall containing Doc back up vertically, Washington again attempts to interrogate him. After being repeatedly hit by the Meta and threatened to be shot, Doc reveals that Simmons said something about a distress call, and mentioned "sand". At the desert, the Reds spy on Epsilon-Church and Caboose. Sarge believes that the Reds may be able to restore the Blues to command's database at the facility mentioned by Epsilon Church. As the Reds leave in pursuit, Tucker takes the opportunity to escape from the aliens and follows the Reds. Epsilon Church and Caboose arrive at the entrance to the facility, hidden within a derelict factory, and find a monitor embedded in a tree. The monitor activates and a voice identical to that of Sheila is heard, explaining that they have 30 seconds to leave or be killed. When Caboose asks if it is Sheila, the program identifies itself as F.I.L.S.S. (Phyllis); Sheila's name before Church mistakenly renamed her during Episode 50. Upon hearing Epsilon Church's voice, Phyllis disables the countdown, believing him to the the Director of Project Freelancer. At his request, Phyllis opens the door to the facility, which was hidden in a wall. As the episode ends, Epsilon Church asks Phyllis to answer to the name Sheila, as it will be easier than getting Caboose to adapt to the new name.

The episode starts with Church and Caboose entering the Freelancer base and having F.I.L.S.S activate the tutorial tour of the base upon Caboose's request. It turns out to be a Freelancer storage facility and on part of the tour F.I.L.S.S reveals she has no knowledge of the Blue Team. They then head to a door that only the Director can get access to. However, much to Shelia..erm F.I.L.S.S's surprise, Church has her let him take Caboose in. Meanwhile outside the Reds are discussing on how to enter the base. Simmons suggests that they pose as Freelancers to F.I.L.S.S, and since Freelancers use US states as their names, Grif gets Alaska and Sarge picks "Double-O-hio." Simmons goes with the "State of Denial" but the joke is lost on the other two. Meanwhile at the desert Washington and Meta have arrived with Doc (still stuck in the wall) dragged along. Wash then instructs a disgruntled Meta to dig in the sand which is burying Doc slightly. Meta then stops to reveal the helmet of C.T. Wash then take a look and is shocked to see it and wonders why she is there. They then turn to see the group of Aliens found them. Back at the Freelancer base Church and Caboose come have found that the restricted room is full of duplicates of Church's old body (to a happy Caboose as he can bring back Church). However that is not why Church is here, he then opens a storage chamber it appears he is disappointed at what he saw.

Agent Washington and Meta are still trying to get Doc out of the piece of wall. They throw a couple grenades and it finally breaks and releases Doc. Meanwhile, the Reds have made it past F.I.L.S.S., thanks to Sarge's "contingency plan" which not surprisingly, involves the business end of his shotgun. They hear a sound deeper inside the facility and go investigate. Back in Sandtrap, Wash, Meta and Doc come up to the aliens, who Doc says is drawing them a map in the sand to where Church went. The map is nothing but an insult that says "humens suk." Wash and Meta open fire on them. The Reds find that the sound is Caboose standing outside the door he and Church went into, and Caboose is telling F.I.L.S.S. to keep it shut. Inside the room can be heard Church yelling at something and several explosions. Something starts pounding on the door and Caboose leaves. The Reds stand there confused thinking of a plan while the door is busted down. When the door is destroyed, out steps none other than Tex, who pounds her fists together and asks "who's first?!"

F.I.L.S.S. starts to sound the alarms stating there is a security breach on level 'Alpha.' Tex soon chases the Reds out of the base and soon starts to beat up the reds and Simmons is separated from the group. Simmons runs to Caboose, who is in a control room, and tell him he needs a bigger weapon; Caboose presses random buttons until a rocket launcher falls down to Simmons. Simmons runs into Tucker who recruits Tucker to help distract Tex. Sarge and Grif are still getting beaten up by Tex, until Tucker pulls out his sword and draws Tex's attention away from the Reds. However Caboose accidentally 'saves' Tucker, and yells at Caboose for fucking up the distraction. Tex realizes that Simmons fires a rocket at her, and throws a teleporter door at the rocket, redirecting it at Simmons blowing up the area he was standing on. Soon Tucker, Simmons, Grif and Sarge are rejoined to attempt to fight Tex as Caboose still tries to find ways to 'help' them out while in the safety of the control room. After some major ass-kickery, Tex ends up throwing everyone, but Tucker, to the other side of the room where. Caboose then attempts to drop a crate, which Tucker and Tex are under, in order to help Tucker. After Tucker dives out of the way, Tex catches the Crate and throws it at Tucker and the reds. Tucker is able to slice the crate in half missing himself as Grif and Simmons are hit by the split ends of the crate and Sarge is covered in Med Packs. After Tucker attempts to fight Tex, he his sword stripped from him and repeatedly gets thrown into teleporters, slowly getting black stuff all over his armor. Realizing that the rocket launcher is an older model, Simmons attempts to fire it at Tex, but can't tell Tucker and Tex apart. After Simmons fires a rocket at Tex, she preforms some acrobatics in order to avoid being hit by the missile that is chasing her, running through teleporters to avoid and redirect the missile. After coming out of the teleporter unscratched, Tucker and the Reds get caught in the explosion propelling them across the room. Soon after they are down for the count, Tex gets hit in the head by the monitor and Church tells her to pick on someone her own size, as the camera turns to see Church in robotic armor.

Tex is bashing Church's original blue body with the Monitor body he had been using until recently. Caboose talks to F.I.L.S.S. who says he should use the "armor lock" function to get Tex to stop, which was developed when the Freelancers broke into the facility. He does and it locks Tex down and makes her stop, but it then also locks the Reds and Church down as well. Meanwhile, in Sandtrap Agent Washington and Meta have killed all the aliens. Wash tells Meta to search the camp for where Church went. Doc and Wash discuss the paid benefits they get for working; Wash is surprised to hear that Doc gets paid overtime when he doesn't. Meta finds something in a cave and Wash tells Doc to go inside and check it out.

Church is in Recovery Mode since Caboose activated armor lock and disabled their movement (except him because his Mark V armor is out of date). Church and Tucker then get out of Armor Lock. While in Sandtrap, Washington, Doc, and the Meta found Epsilons body. The Reds are also stuck in Armor Lock, but they think they're dead. They talk to Church and agree to not attack the Blues, and F.I.L.S.S. gets them out of Recovery Mode.

Washington, the Meta and Doc gather near the Epsilon unit, which Washington realizes is empty due to the AI being moved to the eye-like body they saw in Valhalla. Doc, having not seen it, thinks Washington is going crazy from heat-stroke and tries to psycho-analyze him while the Meta begins converting the storage unit into a capture unit to retake Epsilon. At the facility, the Reds and Blues debate reactivating Tex until Church takes AI form and inserts himself into her body. Once there, the two bicker for a bit until Church agrees to let her out and hit Tucker for making an ex-wife joke earlier. Back in his body, Church has F.I.L.S.S disable the recovery mode on Tex, who gets up and smacks Tucker.

The Meta finishes configuring the old Epsilon unit into a capture unit. Out of curiosity, Doc asks Washington if they could track the Reds' trail, like heat signatures, footprints etc. But Washington tells him otherwise, however, after doc is out of earshot, Washington asks the Meta if they could track the Reds like Doc suggested. Back at the facility, Tex fully recovers and discusses Epsilon/Church's motives on freeing her. In an awkward attempt, Church claims that he needed to get Tex out of his head and even refers to her as his girlfriend. Meanwhile, the Reds decide to use the absence of the Blues to put them back into the database. Simmons and Grif decide to go together, after Simmons threatened to change Grif's job description and change his gender to a woman. Back at the desert, Doc finds out that Washington has taken his suggestion an had Meta find the Reds successfully. Doc simply demands that the two give him credit for the idea.

Tex and Simmons are trying to obtain information from F.I.L.S.S. when Epsilon-Church walks in. When Church explains that Sheila keeps calling him the Director, Tex explains that there are no profiles on the Director, Church, or herself but everyone else has one. After this Simmons leaves to tell the Reds that he found out that Washington used to wet the bed. She then points out a Freelancer base somewhere in an icy area. As Tex leaves, Sheila asks Church (still thinking he is the Director) to make a journal entry. Church asks her to play one as an example. Realizing that these entries might contain answers, Church asks Sheila to transfer them to his armor and then delete the rest. Meanwhile, Grif tells Sarge that Simmons is "doing inventory stuff". Sarge asks him why he isn't helping and Grif responds saying he is on break. Sarge explains to him that "you're always on break." After back and forth arguing Grif finally goes to Simmons. Tex comes back with new armor as she prepares to leave for the icy Freelancer base. Though the other soldiers want to come, Tex only agrees to bring Church instead. Grif finds that Simmons found the devices that enable the Freelancer agents' special abilities (invisibility, time distortion, etc). Grif asks Simmons to suit him up so he can take an invisible nap.

After dispatching the guards by her lonesome, Tex and Epsilon-Church arrive at the Freelancer base. Church has another flash of Valhalla, and realizes he mixed the two locations up in his memories. Tex reveals that this was where Alpha was sent after the very first break in, and it was here more and more "tests" were run on him. Other AI were used in the torturing process of Alpha, with Omega and Gamma being used to create tests that Alpha would purposefully fail, driving him mad, and breaking him to the point he could not recognize anybody, not even Tex. When Church asks if she and the other Freelancers succeeded, Tex says no, and that she failed herself and Alpha. At Sandtrap, Wash asks Doc if he can comment on the Meta's current condition. Doc only reiterates that the Meta has too many power-ups that he can't operate anymore. At the first Freelancer facility, Simmons finally installs Grif with one of the armor enhancements. This winds up being a super-speed ability, which sends Grif into a wall. However the timer runs out as the episode ends and Grif, exhausted, takes a nap.

Informed by F.I.L.S.S. that the storage facility contains backups of Project Freelancer data, Simmons has her restore the Blue Army data. Grif peruses the records, which show that all the Red and Blue bases are merely training grounds for Freelancer agents, and are staffed with the army's worst soldiers. Furthermore, all the strange events they had encountered, including being seemingly blown into the future, meeting the Alien, and Tucker's pregnancy were part of just one of several scenarios that may be run at simulation bases. These revelations shocks Sarge, who walks off and constructs a base from junk. He insists that Simmons and Grif stop calling him "Sir", and then announces that he quits. At the Freelancer base, Tex reveals that she is looking for the Director. She suggests that Washington and the Meta may know who the Director is. In the event they do not know his identity, Tex states that she will simply kill them, and that if she cannot find the Director, she will settle for destroying everything he built. When Epsilon-Church asks how Tex will get in contact with Washington and the Meta, she shoots him, triggering his recovery beacon. She explains that the beacon would not have activated until they left the storage facility. Church insists that he would have helped her. She states that he cannot even help himself, which is why he made her. Church asks her why she is doing all this, and she says that she intends to find out. In the desert, Washington and the Meta pick up Epsilon's recovery beacon. Washington has the Meta grab the storage unit and Doc acquire a vehicle, stating that they are "going to the only place that's left."

Washington, Doc and the Meta arrive at the freelancer base where they discover Epsilon unconscious and fall into a trap set by Tex. Caboose learns of the recovery beacon and tries to get help, prompting Sarge to rally the Reds and Blues together to save Church and Tex from Washington.

Wash start waking up after he was unconscious by Tex's attack. On seeing her approach, Wash crawling toward his weapon, but Tex stopping him. She asks him where's the Director, to which Wash says he doesn't know. Receiving no response he wanted, Tex decides to kill Wash, but The Meta hits her, starting a fight between three of them, revealing that Tex had hidden weapons all over the battlefield. Doc comes close to Epsilon to ask if he’s OK, what says no. Following the fight, Tex pops placed bombs at the site, causing an avalanche. Despite the efforts of Wash and Meta, Tex advantage continues to blow up a second pair of bombs placed at the edge of the cliff. Wash and Meta begin to fall, but Wash is saved by retrieving his weapon, while Doc saved Wash by the Warthog’s towing mechanism. The Meta continues attack Tex, but she stabs him with a knife. Meta achieved escape firing his weapon, leaving Tex unconscious, this leaves that the Meta capture Tex in the capture unit. Wash tries to convince Epsilon to surrender, but Epsilon decided to fight against his ex-partner. Wash asks Meta that give him the captured unit, but Meta, blinded by the power and vision to finally have an AI after he had lost, betray him and install the capturing unit on his back, turning on his cloaking unit. Wash tells Doc that protects Epsilon while he is in charge of the Meta, but Meta overthrow him. Meanwhile, the Reds and the Blues come in a Pelican, shattering it on the battlefield, getting away the Meta to instead. Epsilon and others find the drive where Tex and want release her, but Washington says he cannot release her if it has the necessary tools, so he tells Tucker and Caboose retrieve tools inside the base, while the Reds find objects that have the power to liberate Tex. As teams will search, Epsilon tells Wash that he’ll become immersed in the unit, but Washington says it does not because it is their only ticket out of jail. Epsilon says he will do it for him, for Alpha and for the Director. Epsilon reveals that it has begun to remember his past after reading the Director’s diary, which refers to the person whom the Director loved. Wash reveals that person's name is Allison, Epsilon responds "she returned when Alpha was created”, which Tex is really a bio-product of the Alpha's creation. When Wash call her a "shadow" of the real Allison, Epsilon is angry with him. While still speaking, it reveals that there have never been alone... the Meta had been camouflaged behind in the snow, making others believe that had separated from the capture unit.

Finale to Revelation.