This page contains spoilers
Plot
As depicted at the end of episode 1, Rhys and Fiona activate a device that provides a map of Pandora as part of the Gortys Project. Rhys becomes startled (as the player knows, due to him seeing a ghostly vision of Handsome Jack) and runs off. The other three characters attempt to take a closer look at the map but end up inadvertently closing it. This seems to alert a nearby terminal that is requesting a retinal scan and Fiona is presented options. The computer only accepts specific scans and threatens to alert a General Pollux. Hearing a beeping sound, Pollux is found in a box somewhat resembling a coffin. The characters are unable to remove the body from the box and Sasha suggests removing the eye. Fiona accomplishes this with a spork. After the retina scan is complete, the computer plays a video log from Athena sent from the town of Old Haven, followed by a message from Pollux urging any viewer to release him from suspended animation. As the characters realize they have inadvertently killed him, Rhys falls off a railing and onto the floor, covering the characters in a blood bath (an event that Rhys disputes).
The scene briefly moves forward back to the Stranger holding Rhys and Fiona hostage, and we now see Rhys' version of the events. After Handsome Jack appeared, Rhys follows him up the stairs and Jack becomes annoyed with Rhys' talking. Jack is unable to rip Rhys' throat out and doesn't understand why. Rhys explains that he is only a hologram, the real Handsome Jack died years ago. The actual conversation is determined by the player. A second attempt to remove Rhys' throat causes Rhys to back up and inadvertently fall backwards over a rail to the lower floor and hits his head with an impact that should have knocked him cold (and was not nearly as bloody as Fiona suggested). It also causes Handsome Jack to disappear.
Moonshots (missiles) are being sent from Hyperion to the bandit hideout where the characters are located and they escape in Felix's nearby caravan. During the escape, the caravan is pursued by a Rakk Hive. With some deft maneuvering, Rhys is able to trick the Rakk Hive into taking a fatal moonshot, but he and Vaughn become separated from the girls and the story focuses on Rhys. Handsome Jack reappears in his holo form visible to Rhys only and Rhys attempts to either explain it to or hide it from Vaughn. After contact with Yvette on Helios, the characters find themselves face to face with Vasquez who orders them to dig their own graves at gunpoint. The conversation changes based on player input but eventually ends with Rhys and Vaughn escaping and being chased by Vasquez.
Who should show up but their pal Loader Bot (well, "pal" depends on the choices the player made with Loader Bot in previous encounters). Rhys and Vaughn discuss whether to go to Old Haven or Hallow Point but the choice is left up to the player. Loader Bot flies them to the one chosen.
At this point, the scene briefly goes back to Fiona, Rhys and their captor. Bro, Bro, Bro, Bro bro bro, Bro, you know Bro? "We do not talk like that!" Rhys complains.
If Rhys and Vaughn head straight to Old Haven, they find the facility nearly abandoned. Rhys looks around and finds three power boxes. Player has to figure out how to get them working. Once it's done, several buildings rise up from the ground and players will see a large door that says Atlas on it. August shows up with thugs and has Rhys at gunpoint. Together they enter the building.
After a failed attempt to keep Rhys and Vaughn from flying out of the partially disabled caravan, Fiona and Sasha find themselves alone. They limp the caravan into a small town and find a shop owned by Scooter. After looking around (look for the loot box by the vending machine) Fiona runs into Scooter and needs to come up with a story to get Scooter to fix the caravan. After the player decides the conversation the player will get to decide on a replacement skin for the caravan costing between $0 (just fix it) to $1000. Fiona and Sasha leave the shop on foot and head towards Felix's nearby house. After entering the house, the player will need to search the house and locate a safe. Remove the items including a black light and use the light to search the house again for clues. Locate the loose boards on the floor and remove them. A video message from Felix reveals that a powerful crime boss named Vallory has placed bounties on their heads, and his doublecross was really a failed attempt to spare the girls from her wrath. Remove the lock box that is hidden in the floor and go through the contents. There will be several items including an upgrade for Fiona's gun. A couple of bounty hunters named Kroger and Finch break into the house and the player needs to decide how to handle it. After escaping the thugs, Fiona and Sasha grab their things and run, right into Athena, who is also seeking to collect the bounty.
If Rhys and Vaughn decided to go to Old Haven, Fiona hurls a stun grenade at Athena, incapacitating her long enough for the girls to head back to Scooter's shop where they see the fixed/upgraded (depending on players choices) caravan. After realizing Athena was still after them, they (depending again on choice) force their way back into the shop with Athena protesting behind them. Players meet Springs who turns out to be Athena's girlfriend. At this point Athena has removed her hood and hidden her shield and pretends that she knows nothing about an assassin nearby. Players get to decide whether to go along, or state that Athena IS the assassin. Athena warns them that there are worse people out there who could be looking for them. Fiona and Sasha leave and head toward the location of Rhys and Vaughn. They also have the option of taking Athena's shield: doing so will incite no reaction at the time as Athena is unable to reveal her actions with Springs standing right next to her.
They arrive at the Atlas site and notice the devastation. Regardless of player comment, Fiona believes that Athena made the mess and that they may have just gotten lucky 'back there'. Then they see the open door and walk inside where Rhys and Vaughn are being held at gunpoint by August and his thugs. After the player decides what to do, Vazquez shows up to the party.
If Rhys and Vaughn decided to go to Hollow Point, then Loader Bot battles Athena, forcing her to retreat. Fiona and Sasha find Rhys and Vaughn at Scooter's, trying to convince the latter that they own the caravan. Upon spotting Fiona and Sasha, Rhys refers to them as their friends. Fiona can either confirm or deny it. Either way, the four leave for Old Haven (with Athena watching them from Scooter's roof), and the events that would have occurred to Rhys and Vaughn had they gone to Old Haven in the first place play out, only with Fiona and Sasha present. This time, all four enter the Atlas building, only to be met by August and Vasquez.
Loader Bot is commanded to attack Vasquez (either by Vaughn or Rhys) and Vasquez shuts it down using a universal remote. Vasquez heads down a corridor with Rhys and the unseen holo of Handsome Jack and August takes Fiona down another. Both characters have their Gortys pieces with them that they found back in the Gortys lab. Sasha and Vaughn are left behind, guarded by the thugs.
Handsome Jack is trying to figure out how he knows Vasquez while Vasquez is yapping away about how he made it to the top and how Handsome Jack would always make time for him and punch him in the face (apparently a sign of affection?). Vasquez punches Rhys in the stomach as an example. The scene switches to Fiona and August and players control the conversation. If players ask why August is doing 'this', players will learn that August screwed Vallory by doing the vault key deal under her nose and now August has to convince Vallory that whatever the Gortys device leads them to, that it's worth more than the Ten Million that August never got. He hopes that this will keep Vallory from killing him. Then August asks about Sasha.
Now players are switched back to Rhys where Vasquez is still yapping away. Suddenly Jack remembers and realizes that Vasquez used to be the bald headed man in the mail room who was getting hair implants. (Vazquez has a full head of hair in the game). Players get to choose whether or not to make fun of Vasquez and ask him about it. At the end of the corridor is a device that players will need to interact with. This puts up a shield, separating Vasquez and Rhys.
August walks Fiona to the end of their corridor where she will need to interact with the console as well. This also activates a shield and now she and Rhys are moved together on platforms and must connect the consoles together. They are reminded that their friends are still being held at gunpoint. After putting the consoles together, a round metal electronic ball is created and is floating inbetween them. As Rhys reaches for it, it becomes compromised and several security bots show up surrounding them as well as their party who are still inside the building. Fiona wants to use a stun grenade on the bots while Jack offers to use the electronics inside Rhys' head to disable the bots if Rhys will let him have access. The player must choose and the resulting cinematic ends the episode.