Sophia

Sophia is a female-presenting alien who is thousands of years old. She is able to transfer herself into lines of code in a computer system. Her main goal in Chrysalis is to wipe the memories of humans trained with the muscle memory to dig up a rare element only found on the planet Mars. Due to the nature of her residence in anything with electricity, she is unable to reach Mars herself and must rely on the Nemesis children she salvaged from the Programs.

Before Chrysalis
Less than 100 years before the Programs finished, Sophia found the space station Chrysalis orbiting Mars. She took over the system and shut down the self-sufficient AI, Skippy, who had been running for over one million years. She figured out the Project Nemesis plan and decided to wait for the various groups to finish their simulations before utilizing them for her own gain. She may or may not have been responsible for building the Terrarium.

Chrysalis
Sophia initially presents herself to Nemesis groups 1 and 3 as a stone-faced woman with black hair and an ageless face. Min Wilder guesses that she's somewhere between twenty and forty. She then explains the testing process to them. Later, she attempts to make a deal with Min, telling her the truth about Mars and coercing her to get her classmates on board with the testing.

Once the initial testing is finished, she then begins conducting interviews, but this is interrupted when Tack Russo discovers that there are multiple copies of Sophia all around the ship. He then organizes a breakout attempt to save Min, but Sophia rallies her forces and puts a stop to this. In the process, it is discovered that Sophia is an alien consciousness and is truly the one controlling Chrysalis. She puts Tack back in the testing process and offers one final deal to Min: deliver Noah Livingston to her or die. Min, even now knowing what repurposement truly means, refuses.

Min's friends break her out and lock Sophia out of the command module. They then restart the AI, distracting Sophia while they set bombs along the outer ring of Chrysalis. At the very end, as the station is falling to pieces, she corners Min, Noah, and Tack, revealing to them that the only copy of her existence is standing right in front of them. Noah lunges for Sophia and overloads his blaster gun, sending them both into space.

Sophia may not be truly deceased. Since she is an alien, it is unknown if death is a viable option for her species, but it is clear that she needs a host to operate freely. The members of Livingston Colony decide to go without technology, concerned that part of Sophia is still hiding somewhere in the hardware of a ship system. Tack finds no sign of her as he is rebuilding the regeneration units to resurrect his classmates, but she may still be in the system somewhere.