After Dr. Nicholas Rush was abandoned on the Gravel pit planet, he managed to access the database within the downed alien ship. However, in doing so he triggered a distress beacon. Rush was then discovered and captured by the Nakai. They probed his mind for information, and he claims that he was able to resist their attempts somewhat.
Sometime later, Colonel Everett Young used the Long-range communication device to contact Earth about Rush's supposed death. However, as one of the aliens had recently handled a Long-range communication stone, Young ended up swapping bodies with that alien instead. Once the Destiny left FTL, the Nakai mothership showed up. (SGU: "Justice", "Space")
- ―Alien's response to Eli's greeting[src]
Eli Wallace suggested sending a greeting to the alien vessel, and did so. The aliens sent a short message back, in English: "Surrender." It then launched around a dozen Nakai fighters to attack Destiny. Colonel Everett Young dispatched Lt. Matthew Scott and MSgt. Ronald Greer in the Ancient shuttle to intercept the fighters while Eli brought the weapons online.
The fighter compliment headed straight for Destiny, almost completely ignoring the shuttle despite several being destroyed. One of the fighters docked on Destiny's hull while the rest provided cover. Chloe Armstrong was kidnapped by the boarding party and the aliens retreated to their mothership.
Young used the Long-range communication stones once again in order to infiltrate the vessel and rescue Chloe. Instead, he found and released Dr. Nicholas Rush. Rush instructed him in the use of the Nakai mind probe, which gave Rush a basic overview of what had happened since his capture. The mind probe also had the effect of breaking the communication stone link. With the link broken, Rush used the probe once more to learn about the ship, then killed the alien.
The mothership attacked once again, and Young ordered Eli to use the main cannon to destroy the vessel. Rush managed to free Chloe and escape in a fighter during this time, and the mothership retreated soon after. (SGU: "Space")
With the return of Dr. Nicholas Rush to the ship, the Destiny expedition learned of the Nakai's interest in Destiny. It also had ramifications on the mutiny that happened soon after. It's also later revealed that the Nakai infected Chloe Armstrong with a pathogen that alters her until its removed during the Drone attack on Destiny. (SGU: "Divided", "Pathogen", "Deliverance")