The Intruder

During a close pass from an alien probe/fighter/ship the frigate Renowned is infected with a computer virus. There is a spike of power while the virus attempts to gain system access to the medical lab. A doctor investigates and is killed by a powerful electrical spike.

The investigation reveals the security camera footage is blank 30 seconds before the fatal spike in power.

The doctor was having issues with the medcomputer and ran a diagnostic, he then started enabling certain computer security protocols designed to isolate and shutdown corrupted programs. 

You ask, "What programs." 

Answer, "That's just it, I don't know. He was killed before running them."

Trying to trace the source of the power spike that killed the doctor results in another death of someone in the investigation team. Nobody may have known where the investigation was taking place, however security cameras would have detected the team. 

If the virus does not gain control of propulsion and navigation it will infect the communications equipment and send a distress call to its creators. Ingenious characters may try to blow up or shoot the communications array to stop the distress call. 

Note: The goal of the AI is to fly the ship to a destination where it can be picked up by the AI developers. 

Virus may take over fighters, shuttles, etc. Anything with a computer and enough memory. AI will download a copy of itself into these ships. If the main computer is shut down and restored from backup the virus living in the fighters/shuttles can re-infect once ship comes up to full power. 

If the PCs continue to thwart the AI it may try to pass near a star in hopes of burning/radiating the biologicals in the ship.