The plot of Ikaruga is... sketchy and ill-formed (as well as being found almost entirely in the manual). In classic SHMUP fashion, it essentially boils down to "blow everything up, including (and especially) the source of the bad guy's power". This is all pretty quickly forgotten until the very end of the game, when you defeat what seems to be the final boss.
|Which is already not something you'd call.... easy.|
After absorbing hundreds upon hundreds of bullets over the course of the minute, your ship pulls back, and in the final cutscene, unleashes the most awesome salvo I think I've seen in any videogame. Your ship (and assumedly, you) are destroyed in the process, but the object (which the plot calls the "Stone-Like") is destroyed as well. Next to no explanation is given, and the game simply fades to white. A fitting end to a beautiful and jaw-droppingly difficult game.
Now, since this game is brutal on easy mode with a fair number of continues (which remains the only way I've beaten it, though I'm loathe to admit it), here's the full final level, complete with the final cutscene. The player is... quite good. Check out the game of ping-pong you have to play with the boss before the end boss starting about 2:20 into the video and ratcheting up to ridiculous levels around 2:38.