This is one of the game's two secret bosses (the other being the Anti Freaks fight, which wraps up the 100% subplot). This boss can be accessed by beating Moon Secret, which itself can only be opened by beating all the previous secret levels.
The Kranion's Secret Weapon in question is his Skullmobile, which can be seen in the intro. This was the final boss in the 2016 Remaster, and is one of the very few things that made it over to Ultimate relatively unchanged. I definitely have some rebalancing to do--it has too much HP, and I wanted a glowy effect for the giant lasers and not a blinking one, but these shouldn't take too long to do.