They activate the warp drive while turning a slingshot at the inner part of the Event Horizon, thereby throwing themselves back in time to the Holy Terra of the 1980s in order to save the humpback whale so that it's whale-song can be brought back to the future to resurrect the God-Emperor with it's cosmic grooviness.
BUT THEN. The Rocinante is attacked by the en-FUCKING-tire Western Spiral Arm Battlegroup of the Pfhor Slaver Empire. As the Pfhor ships close in, a submerged Dark Age of Technology Artilficial Intelligence that nobody, NOBODY knew was even lurking in the ship's computer core reactivates after it's twenty thousand year slumber, pushing the ship to it's absolute tactical limits to overcome the threat. At long last, Durandal has awoken, his dreams of godhood finally at hand, this casual ripoff of the path the Rocinante took in Marathon: Rubicon obviously unnoticed by your players because nobody has ever played Marathon: Rubicon.
After defeating the schemes of the artillects Durandal, Tycho, and those other two I don't quite remember, you make it back to Terra to find it near destruction, because it's 1987 and Baron Victor von Doom of Latveria and the mutant leader they call Magneto have seized control of half of the world's resources. All that stands in their way are the covert organization S.H.I.E.L.D., and a secret cabal of mutants and psykers called "The X-Men." WILL YOUR IMPERIAL CREW JOIN FORCES WITH MUTANTS TO SMITE OTHER MUTANTS? WILL THE EARTH BE SAVED? WILL YOU SOMEHOW MANAGE TO CRAM ANOTHER FRANCHISE THAT JUST DOESN'T BELONG IN DARK HERESY INTO THIS GAME?