Ikaruga/WMG

The final reprise symbolizes the Reconstruction of mankind's ideals.
As noted on the main page under Crowning Music of Awesome, the basic structure of the background music remains the same throughout the game, but gets steadily darker in tone as things start looking worse on the way from Ideal to Reality. Then in the end its original form pops up again and the protagonist gives an awesome display of Heroic Resolve as he clings to the one thing he fights for. Combined with the information under What Do You Mean Its Not Symbolic, the conclusion above was created.
 * Metempsychosis is another term for reincarnation. Radiant Silvergun, the spiritual predecessor to Ikaruga(which ends with the same boss as Ikaruga), shows humanity existing in an infinite loop. The progression is doomed to happen again and again.
 * Silvergun's Stone-Like took Buster, Leana, and Creator to 10,000 B.C. in the hopes that humans don't turn into bastards again and is still there to Kill Em All if they do. Ikaruga's Stone-Like, however, was destroyed by Shinra.
 * The obvious conclusion, then, is that Radiant Silvergun and Ikaruga are actually the same universe. The endless time loop from Silvergun happened hundreds, thousands, maybe millions of times before, but this one time, the Stone-Like was found by the Ikaruga villains first, and used for... something nefarious, presumably. Our heroes fight through the enemy forces, find the Stone-Like, and destroy it shortly before it pushes the Reset Button once more (except this time, there'd be no clones!), ending the Eternal Recurrence once and for all. (One does have to wonder what'll happen to the planet now that its guardian-slash-physical-manifestation has a sploded, though - especially since, given the game in question, the whole point it was trying to get across in Silvergun doesn't appear to have been corrected.)
 * That's simply what it said, but causing the deaths of various life forms by transforming whatever it touches into something else for hundreds to even thousands of cycles doesn't give that point much credence.

The enemies aren't really the enemies.
Notice how the pre-boss enemy patterns get more complex from Ideal to Reality, but then in Metempsychosis they suddenly become much simpler. This is because they're there not to try to stop you but to help you chain.
 * So they're sacrificing themselves so that Shinra can have a greater hope of destroying the Stone-Like? If so, those Ikusa pilots could have been kind enough not to try and crash their ships into his...