A few ideas:
Sample 217 gets curious and naturally manages to figure out she's in a simulation. Coffee reminds her that her physical form is dependant on this simulation to survive. But curious and bored of this simulated world she finds a way into the core of the facility's computers where she discovers a way to upload her own consciousness into the mainframe becoming the brains of the facility. Not wanting this for 217 and knowing she doesn't truly understand she'll be stuck like that forever have to carry this burden and never be able to have a corporal experience Coffee sacrifices himself and becomes the ships new AI.
Grief stricken at this 217 tries to apologise but Coffee just tells her he could never be mad at her as he reactivates DCo-09 who awakes in Coffee's body and then orders him to be 217's guardian. The reunion is short lived however as it's revealed Lun Infinus is heading towards a black hole and in order to escape they will need to build a ship.
This will require the help of the Derelicts but they are all deactivated and there is barely enough power to last one day so DCo-09 and 217 must work together to repair the solar panels with the player switching over to Dco-09 in the real world and then 217 in the virtual. After a sufficient amount of power is achieved the Derelicts awaken and get to work with 217 and DCo-09 helping until after a number of bosses and levels as well as a time limit which starts for real once the Derelicts awaken a ship is created with Amos uploaded into it to become the navigator and the small ship is full of storage for everyone to download their simulated worlds and themselves into it.
The final day approaches and 217's consciousness is the last to be uploaded but in a sudden panicked realisation asks DCo-09 what will happen to Coffee who is still presently uploaded into the facility. In a moment that is both heart-wrenching and funny Dco-09 uploads into the mainframe and much to Coffee's chagrin and worried shock manages to switch places with DCo-09 sacrificing himself as Coffee back in his own body hurries to the ship as the station plummets into the black hole and everyone is saved thanks to DCo-09 who briefly wonders if they play games in the afterlife as he is sucked into the unknown.
The game ends with the ship landing on another equally mysterious planet and everyone is at peace inside the ship's simulation except for 217 who now inhabits Coffee's body and ventures outside the ship into the beautiful cosmic night with the camera panning to a screen reading 'DCo-09: active' as Coffee in his human avatar form looks on in pride.
