This will be an au-heavy verse since the Prisoner does not survive in the game.
This verse can occur before his people found the Eye of the Universe and cloaked its signal.
Can also be during the game-period. Maybe he broke out and traveled with the Hatchling for a few cycles before the Hatchling found the Eye of the Universe. I don't know, it's video game logic. Anything can happen.
Taken from the Wiki:
Like the other inhabitants of the Stranger, the Prisoner lived on their home moon, a terrestrial world that orbited a gas giant. At some point, they received the signal from the Eye of the Universe and demolished their home in order to build a massive artificial ring world to reach the Eye. They traveled to the Eye of the Universe and after analyzing it, they found out that interacting with it would lead to the death of the universe and all life. Determined to prevent this, the Stranger's inhabitants built a spacecraft designed to block the Eye's signal. With the Eye's signal no longer being able to broadcast out into the universe, the Stranger's inhabitants went to sleep in a simulated reality of their homeworld.
However, the Prisoner woke up from the simulation after some time. They went to the signal blocker's controls and deactivated it, freeing the Eye's signal. Shortly after doing this, the other inhabitants caught them and locked them into a sealed vault blocked by three seals both in the Stranger and in the simulation, along with an artifact that allows entrance to the simulation. They then built a structure around the vault and submerged it in the Reservoir. This led to the Prisoner's eternal confinement in a separate part of the simulation. As time went on, the Prisoner and all others of their kind died, but their minds were still alive in the simulation, unable to wake up.
The Prisoner's actions had far-reaching consequences. Immediately following their imprisonment, the other inhabitants uploaded all their slide reels into the simulation. They then burned most of the slide reels in the real world, apart from a select few reels of which they only burned specific slides. A portrait depicting the Prisoner in a house in the Cinder Isles was scratched out. Lastly, the Prisoner's house in the simulation in Starlit Cove was burned down.
The Stranger's inhabitants also re-enabled the Eye signal blocker after locking the Prisoner up. They destroyed the control mechanism for the blocker to prevent anyone else from using it. This broke the connection between the Stranger and the blocker, meaning it could no longer be disabled. Nevertheless, for the brief amount of time that the Eye was able to send its signal, the Nomai of Escall's clan were able to receive it. This eventually led to them constructing the Ash Twin Project.
After learning the three glitches in the simulation from all Forbidden Archives, the Protagonist can extinguish the seals on the Sealed Vault in the simulation. This opens the vault, which the Protagonist can enter to encounter the Prisoner. The Prisoner is initially surprised upon seeing them. They subsequently use a Vision Torch to show the Protagonist the actions they took that led to their imprisonment.
When they have shown this, the Prisoner gives the Torch to the Protagonist. The Protagonist can use the Vision Torch to show the Prisoner what happened after their imprisonment. The visions that can be shown depend on the Ship Log's completion. The Prisoner lets out a howl after seeing the visions, upon which they take the Vision Torch and bow to the Protagonist. They use the elevator to exit the Sealed Vault. If the Protagonist follows them up, they can find the Prisoner's Torch near the water, with one final vision showing the Protagonist and the Prisoner getting on a raft and heading towards the horizon. There are footsteps on the ground leading towards the water, showing that the Prisoner has walked into the water to let their Artifact go out.
If the Protagonist has tried to talk to the Prisoner on the Stranger, they can find the Prisoner during the finale after they have entered the wormhole on the Eye of the Universe. When gathering the rest of the travelers, the Prisoner can be heard playing an instrument that sounds like a theremin or musical saw. They initially stand a distance away from the campfire, where they ask the Protagonist if they are allowed to join at the campfire. If given permission, they join the rest of the group at the campfire and play the main theme. This conjures endless possibilities from the smoke of the fire, which are observed and then collapsed by the Protagonist into a single reality.