Daniel Remar (of Iji fame) has released a sequel to one of his older games recently, and like his other games, it's freeware.
Hero Core follows Flip hero as he faces off against his nemesis Cruiser Tetron for the last time. Along the way he blasts his way through a huge assortment of enemies and bosses, all in the name of ending the conflict for the absolute last time.
Those familiar with Metroid will be right at home with Hero Core. The game plays in a very non-linear fashion, and you can, in fact, fight the final boss from the very beginning. It's not very advisable, though, and there are plenty of ways to upgrade yourself. Once you finish the game, a bunch of extras unlock as well, adding greatly to the replayability. It's pretty difficult, though, so try not to get too flustered or frustrated!