Continuation of Soukyuu no Fafner: Dead Aggressor - Exodus.

2199 AD. Yamato tried to leave behind the Large Magellanic Cloud galaxy, after receiving a Cosmo Reverse System at its destination, Iscandar. However, suddenly, it encounters a mysterious group at the edge of the Large Magellanic Cloud. The crew finds out that the group is called the Gatlantis, and that its leader is the Gutaba expeditionary force commander who calls himself Goran Dagaamu of Thunder. The commander demands that Yamato be handed over to him. Yamato, wanting to hurry to Earth, escapes the fray. However, Yamato is attacked by a devastating beam weapon called the Flame Direct Attack Cannon that can transcend space. Yamato was able to retreat, but ends up getting lost, and finds itself in a strangely colored irregular dimension. The crew decides to turn off the engine on the ship, and explore a mysterious planet. In order to collect information, Kodai, Kiryū, Sawamura, Niimi, and Aihara land on the planet. What they saw when they arrived was a ship that was not supposed to be there. Dagaamu chases after the traces of Yamato's warp, and also reaches the strangely colored space. The planet on which Yamato landed was in fact what Dagaamu had been looking for all along. (Source: ANN)

The year is 2148. Two years after the end of the original Fafner in the Azure TV series, Tatsumiya Island and its surviving residents have returned to some semblance of recovery. However, things have become desperate for our hero, Kazuki; nearly blind now, and partially crippled from his battles with the Festum two years earlier, he clings to the promise his fallen friend Soushi made to him to return to the island and set things right again. Kazuki's hopes flare when a lifeform is detected within an unmanned submarine that comes floating into Tatsumiya Bay one night, but the person aboard isn't Soushi; it is a mysterious boy named Misao Kurusu who may not be entirely human, and who claims to have been sent by Sōshi. With Misao's arrival, hostilities break out anew between the Human Army and the Festum, and the Fafner pilots are thrown into the most desperate battle of their lives - this time, with the fate of TWO races riding on their shoulders. (Source: Wikipedia)

Thanks to Professor Yuuko Kouzuki's technology and Kasumi Yashiro's psychic powers, Cadet Takeru Shirogane travels back to his original world. With no time to lose, Takeru aims to enlist Yuuko's help in his world to complete the Alternative IV project—the last hope humanity has against the BETA, an alien species invading the planet. As the anti-BETA project nears completion, Takeru and other cadets graduate from the Yokohama pilot training academy. However, during a test of the new operating system for the Tactical Surface Fighters—the giant combat suits used by humanity against their adversary—the BETA ambush Takeru and his team. Barely escaping with his life, Takeru is left traumatized after witnessing the cruel death of one of his close friends. Losing his will to fight, Takeru flees back to the other world, where he experiences a similar tragedy. According to Yuuko's theory, people from parallel universes are bound to suffer the same fate. As a result, Takeru must overcome his trauma if he wants to protect the ones he holds dear.