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In 1999 the massive alien ship, the SDF-1 crash lands on Earth. Humanity sets aside their differences and creates a global government, having come to the realization that there are alien species out there capable of technology decades, or even centuries, beyond their own. Eventually, they get the ship operational once more. On the day of the launch, however, the Zentraedi attack, forcing the ship into a desperate ploy to lead the battle away from Earth. Due to a lack of understanding of the alien technology, the ship ends up near Pluto, dragging along a good portion of the island that had been its home, and the island's population.
Thus begins a long, painful journey home for the crew of the SDF-1, and the refugee civilians on board. Along the way they make new lives, all the while fighting a desperate war against the Zentraedi.
And when they make it home, the battle isn't nearly over.