As part of an experiment to try and fend Godzilla off using Miki Saegusa's psychic abilities, Miki pilots the helicopter around the Sea of Japan to a J.M.S.D.F. warship, and lands it on the boat's helipad. The helicopter appears several times afterwards, mostly being used to follow and observe Godzilla from afar.
In this film, the helicopter is used when Miki and her friend look for the missing Godzilla Junior, and then is used to follow him once he surfaces and begins moving towards Tokyo. Following Junior through Tokyo, the helicopter is nearly knocked out of the sky by Destoroyah's flying form, but Junior joins the fray to protect Miki. After Junior is killed by Destoroyah, Miki and her friend land the helicopter nearby, but are nearly killed when Destoroyah rises, flies past and obliterates the helicopter with a blast of his Micro-Oxygen Beam.