Captain Yugi Nagata was the commanding officer of the Japanese ship, JS Myoko. Sent to participate in the RIMPAC Naval Exercises, he immediately sparks an altercation between himself and Lieutenant Hopper of the US Navy, beginning at a soccer match for the 'RIMPAC Cup' by kicking Hopper in the face. The altercation continues on the USS Missouri, at a ceremony being held by Admiral Shane to mark the opening of the RIMPAC Exercises, when LT Hopper and Capt. Nagata fight over their disagreements. This lands both LT Hopper and Capt. Nagata in trouble with ADM Shane, who curtly disciplines them in his office before RIMPAC begins.
During fleet movements at the start of the exercise, the aliens land, prompting Admiral Shane to dispatch the Myoko, alongside the USS John Paul Jones and the USS ''Sampson''. After the destruction of the Sampson and the death of the Captain and Executive Officer of the John Paul Jones, LT Hopper takes over as acting Commanding Officer. The John Paul Jones begins an attack run on the alien vessels, forcing Capt. Nagata and the crew of the Myoko to follow and provide support. This 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 is in no mood to assist the young acting CO.
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 alien's 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 by suggesting use of NOAA chart plots of tsunami warning buoys 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 by shredder drones that led to JPJ's destruction. He then assists Hopper and the 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 the newly promoted Lieutenant Commander Hopper at an awards ceremony to honor the crew for their bravery.