For an unknown period of time, the Nakai tried repeatedly to take over Destiny, landing at least two fighters on it at different points. According to Dr. Nicholas Rush, who read the mind of one of the aliens, Destiny repelled every tactic they tried, and though they could keep up, they could not penetrate its defenses.
After the Destiny expedition arrived, one of the two fighters disengaged from the hull, while the other was used to track Destiny's position. After a failed attempt to overthrow Colonel Everett Young, Nicholas Rush was abandoned on the Gravel pit planet by Young. On the planet with him was a crashed Nakai fighter. Rush managed to restore power to the crashed fighter, but in doing so activated a beacon which brought the Nakai to the planet. He was captured by them and brought aboard one of their motherships, where they used a mind probe to interrogate him. A Tracking implant was also surgically implanted in his chest. Notably, they also found a Long-range communication stone among Rush's personal effects. (SGU: "Air, Part 3", "Justice", "Space", "Divided")
- Main article: Nakai attack on Destiny
Colonel Everett Young, during an attempt to contact Earth, accidentally connected with a Nakai through the Long-range communication device. The connection was broken when the alien he switched with attacked Lt. Matthew Scott. As soon as Destiny dropped out of FTL, a Nakai mothership appeared off Destiny's bow. Eli Wallace attempted to communicate with them, and the aliens sent back a one-word message, written in English: "surrender".
The mothership launched its Nakai fighters, which headed straight for Destiny. Scott and MSgt. Ronald Greer were dispatched in the Ancient shuttle to intercept. Despite losing several fighters, the Nakai managed to dock with Destiny and kidnap Chloe Armstrong, who was nearby at the time. They retreated with her as their prisoner.
To rescue her, Young used the communication device to swap with the alien once again. However, his search inadvertently led him to free Dr. Nicholas Rush instead. Rush, unaware of the identity of his savior, instructed Young in the use of the Nakai mind probe. Using it allowed Rush to learn that Young saved him, and of Chloe's plight. The mind probe also had the effect of severing the communication link. Noticing this, Rush read the alien's mind again to understand their technology, then killed it.
Once the communication link was broken, the Nakai attacked again. Young ordered Eli to destroy the mothership. As Destiny fired on the mothership, Rush successfully escaped with Chloe using a stolen fighter. The mothership retreated shortly after their escape. It's later revealed that the aliens infected Chloe with a pathogen while she was held captive by them. (SGU: "Space")
- Main article: Mutiny on Destiny
After the first battle, Dr. Nicholas Rush's stolen Nakai fighter was jettisoned to prevent it from being tracked. Rush also knew of the second fighter still attached to Destiny from the alien's memories, and encouraged a search to find and destroy it.
Knowing that the Tracking implant in his chest will lead the Nakai to Destiny, and unwilling to take the risk of revealing this fact, Rush orchestrated a mutiny in collaboration with Camile Wray, using it as a smokescreen for his activities. After taking control of the ship, he enlisted Eli Wallace's aid in reinforcing the shields to weather the upcoming assault. Meanwhile, Colonel Everett Young had hatched his own plan to regain control.
Three Nakai motherships dropped out of Hyperspace and began firing on Destiny, trying to break through the shields. During this time, Young regained control of the ship and learned of the tracking device in Rush's chest. Lt. Tamara Johansen was tasked with removing it, with the aid of Dr. Brightman from Earth, while he and Eli monitored the battle. The implant was successfully removed and Destiny survived the attack with minimal damage as it jumped to FTL before the shields could fail. (SGU: "Divided")
- Main article: Nakai attack in the void
When Destiny left for the next galaxy, the Nakai were able to take advantage of an oversight which left one of the communication stones imprinted to Lt. Vanessa James, taking over her body and using it to disable Destiny's FTL engine and give them the location of the ship. Two Nakai fighters were also left on the only planet within range of Destiny's Stargate, leaving no avenue of escape for the crew. The crew is unable to repair the damage in time, and two motherships drop out of hyperspace near Destiny launching fighters while attacking the shields. Despite their best efforts, the crew were fighting a losing battle. Left with no other option, Jeremy Franklin used the Destiny interface chair to bypass the damage to the FTL drive and reactivate it, allowing Destiny to escape, destroying at least four fighters as it jumps. (SGU: "Sabotage")
- Main article: Drone attack on Destiny
During the drone attack on Destiny, Chloe Armstrong, infected with the Nakai pathogen, sends a signal that summons three Nakai motherships to the battle. The three ships are attacked by Berzerker drones, drawing most away from Destiny and allowing it to destroy the Control Ship. Two motherships are destroyed in the battle while the last is severely damaged. When the crew captures an inert drone, the mothership threatens the Ancient shuttle, but a deal is struck instead: the crew will focus on figuring out how to beat the drones while the aliens remove the pathogen from Chloe. It is agreed to and Lt. Matthew Scott and Chloe fly to the mothership where the aliens remove the pathogen. Shortly after the shuttle leaves, the mothership escapes to hyperspace leaving Chloe sure that with whatever information the aliens got from her, they will be more determined then ever to get Destiny. (SGU: "Deliverance")