Before we've even begun, Ikaruga already stands out among other shmups in that it even has a backstory, not even mentioning the fact that it's a pretty damn good one. You won't find it anywhere but in the game's instruction booklet, but it's there.
The tale begins several years before the start of the game, on the small island nation of Horai. Tenro Horai, one of the nation's most powerful men, discovered an object deep underground during an excavation project, which was found to have extraordinary power. Using this "Power of the Gods," Tenro and his followers soon began conquering other nations, "in the name of peace" until they had nearly conquered all civilization.
In an effort to free the world of Horai's conquests, a small federation called Tenkaku rose up to challenge his empire. No match for the power at Horai's disposal, the Tenkaku lost battle after battle, and were completely wiped out, save for one pilot named Shinra. Dragged from the wreckage of his fighter after being shot down, Shinra awakens to find himself nursed back to health by the elderly citizens of a remote village called Ikaruga, to which they had been exiled during Horai's takeover. Upon regaining his strength, Shinra pledges to stop the Horai at any cost, and finds that the elderly villagers have built a fighter of their own design, also named Ikaruga.
Far from any ordinary ship, the Ikaruga was designed by an ingenious engineer named Amanai, and built with the help of other aging village leaders. It was the first ship ever built to handle both light and dark energy polarities, and was the first to be capable of switching between the two at any time. The villagers, because of their strong faith in him, entrust the ship to Shinra. In 2-player mode, Shinra is joined in his quest by Kagari, a former Horai mercenary whose life he had spared. Eager to redeem her past, she sets out in her own ship, the Ginkei, to aid him in his cause. So begins the game. Not a bad plot for a PEW PEW PEW title.