Two years after the defeat of the
Innovators, an unknown alien fragment lands on a research station and reactivates it, causing it to head towards Earth. In Celestial Being's Asteroid Base,
Ian Vashti greets his wife, Linda, after her two-year assignment and unloads two new GN Drives and a new incomplete Gundam, the GNT-0000 00 Qan[T].
Marina Ismail and
Shirin Bakhtiar inspect a colony construction facility, but are attacked by assassins.
Setsuna F. Seiei arrives and destroys them. The Earth Sphere Federation sends GN-XIV's, led by
Andrei Smirnov, to destroy the station.
Kati Mannequin arrives on board the Celestial Being station with
Patrick Colasour and encounters Veda along with the surviving Innovators. The newest emerging Innovator, Descartes Shaman, destroys the probe ship, with debris falling to Earth. Soon after, Earth experiences strange events, with electronic vehicles and devices operating on their own.
Billy Katagiri and Mehna Carmine hypothesize that the events are related to the Extraterrestrial Living-metal Shape-shifters (ELS), a metallic alien species. The Federation forces travel to Mars to discover the ELS's intentions, with Descartes heading out first. Descartes and most of the ships and Mobile suits are assimilated, killing Descartes in the process. With the ELS surrounding him,
Tieria Erde self-destructs his Gundam to take out the ELS. The Sol Brave Squadron, led by
Graham Aker, arrive and help Celestial Being escape. Setsuna falls victim to a mental attack from the ELS and is rendered comatose in the middle of battle. After the battle, the Ptolemaios crew and the Earth Sphere Federation discover a moon-sized ELS and determine that it will arrive at Earth in 92 days. Many of the Federation's Baikal-class ships are assimilated by the ELS, who subsequently created their own copies of the technology. Zabanya and Harute arrive to assist the ESF and member forces in battle. Despite the backup, the ELS still overwhelms the allied forces and assimilates many ships and Mobile Suits. Andrei notices one of the ELS ships heading for Earth and sacrifices himself to destroy the ship. On board the Ptolemaios 2, Setsuna lies in a dream-like state, but awakens after seeing the flower that
Feldt Grace gave him. Patrick's GN-XIV is hit by an ELS and is slowly assimilated. He prepares to self-destruct, but Setsuna blasts Patrick's GNX, saving him from assimilation. With a large number of ELS appearing, the Harute is assimilated and
Allelujah Haptism and
Marie Parfacy are forced to eject. Setsuna attempts to communicate with the ELS via the Twin Drive's quantum effect, but it is to no avail as the ELS thwart Setsuna's attempts. Graham, now partially assimilated, sacrifices himself to let Setsuna enter the core of the ELS ship. After Setsuna establishes contact, he realizes the attack was a misunderstanding, as assimilation was the ELS's only means to understand humanity. It also revealed that the ELS's original homeworld was consumed by a red giant star and they began searching the universe for a new home. Through Setsuna's quantum brainwaves, the true intention of the ELS's arrival to Earth is understood and the battle is ended. The ELS uses Setsuna's vision of a flower to alter the superstructure of their mother ship. Fifty years later, the flower is now a deep space station for intergalactic travel, with the ELS co-existing with humanity. Marina, now living in the countryside, is visited by Setsuna, who has become an ELS/Innovator hybrid. ==Box office==