During fleet movements at the start of the exercise, the aliens land, prompting Admiral Shane to dispatch the Myoko, alongside the John Paul Jones and the Sampson. After the destruction of the Sampson and the death of the Captain and First Officer of the John Paul Jones, leaving Lt. Hopper in command, the John Paul Jones begins an attack run on the alien vessels, forcing Nagata and the crew of the Myoko to follow and provide support. This also leads to the destruction of the Myoko. Rescued by a reluctant Lt. Hopper, Nagata is furious about the destruction of his ship and the injuries caused to his crew and as such in no mood to assist the young Acting-Captain.
His attitude is changed during the examination of a captured alien, as Hopper struggles to remove the helmet, Capt. Nagata is the first person to approach and assist Hopper. Nagata then fights against the aliens grip on Hopper when said alien returns to consciousness.
After the alien is retrieved by its brethren, Capt. Nagata assists Hopper and the John Paul Jones crew in destroying 2 alien vessels, and then luring another alien vessel to its destruction. Shortly after, Nagata rescues Hopper from the damaged bridge of the John Paul Jones during the attack that lead to its destruction before assisting Hopper and crew aboard the USS Missouri. The experience changes his and Hopper's view of each other and Nagata admits it was an honor to serve with him when it seems like they will die.
Captain Nagata was later honored alongside Lt. Hopper at an awards ceremony to honor the crew for their bravery.