"You've gotta break it down to build it back up."
Following the events of the game (Tales From the Borderlands), about a good year has passed. Rhys is slowly building up ATLAS again, overtaking anything that Hyperion had started, and pushing for the goal Jack had always wanted but never could achieve, making Pandora a better place. The difference is Rhys isn't going around releasing dangerous vault monsters and killing all vault hunters to do so. While working one day, Rhys gets a call from Fiona, a now good friend. She informs Rhys that while exploring Elpis, Pandora's moon, it has been hit with a series of ever increasing earth quakes. She requests Rhys's help to find out what's going on and if they can stop it before the moon completely explodes.
Accepting the job, Rhys rallys up the old gang, Vaughn, Gortys and Loader Bot, and sets a course for Elpis. Once arriving things quickly pick up as they discover the lost history behind the true story of what happened on Elpis during the DALH attacks. It becomes clear that some things here are still under Hyperion control and more information is needed from subjects that both Rhys and Vaughn have no idea of. Reminded of an old hero, it is now Rhys has to make the choice to reinstall his old Echo Eye, to enlist the help of the murderous Psychopath that is Handsome Jack, and beg for his cooperation in a last ditch attempt to save both Elpis and Pandora. The only issue being, trying to get back on Jack's good side after crashing Helios
into the ground, and killing him, again.
However, bitter as he may be, Jack might be hiding a few things that were better off left forgotten so many years ago. Some of these things find their way to the surface as the AI tricks his host into giving him a physical form. Handsome Jack is reborn once again.
But this time around... things are different.