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- Warning: The following content contains spoilers for TNG - Assimilation² comics: "Issue 1", "Issue 2", "Issue 3".
In ancient Egypt, Rory and his wife accompanied the Doctor in an attempt to track down and recapture an escaped alien criminal who had been posing as vizier to the Pharaoh. Remembering his time as a Roman centurion, Rory was able to drive a chariot while being pursued by Egyptian soldiers. Immediately following this adventure, Rory and the others found themselves aboard the USS Enterprise in 2368, after the Doctor's TARDIS accidentally landed on the ship's holodeck in the midst of a 1940s San Francisco program. (TNG - Assimilation² comic: "Issue 1")
There they met Commander William Riker, Doctor Beverly Crusher and the android Lieutenant Commander Data. After being mistaken for malfunctioning holographic simulations, the Doctor, Rory and Amy were revealed as real and taken to meet Captain Jean-Luc Picard, for introductions and to discuss the strange arrival. Rory and Amy accompanied the Doctor. (TNG - Assimilation² comic: "Issue 2")
The Doctor and the crew of the Enterprise began investigating an allied Borg–Cyberman fleet attacking several worlds, and followed it to Cogen V. There, Rory, Amy and the Doctor accompanied Riker, Data and Lieutenant Worf down to investigate the aftermath of an assault there. Upon arrival, Rory saved Amy from an attack by Cogenian sentry drones; this made them almost equal for times they'd saved eachother. (TNG - Assimilation² comic: "Issue 4")