In order to gain access to the secret boss you must first obtain the Hasaba and Mami Charms. The Hasabi Charm is earned by defeating the original final boss of the game and the Mami charm is obtained by destroying all Sabu Statues in the game.
Once you have obtained both charms, equip them and enter the final boss room to begin the secret boss fight! By this point you should be pretty familiar with how the game is played and shouldn't have too much trouble defeating the secret boss but if you're struggling: I would recommend loading up on some consumables prior to the fight so that you can heal up if you get low on health.
I'm unsure on what consumable is the best bang for your buck but I found lasagna over at the bay area where you fight Noize was pretty good (75% health for $50).
Some Spoiler Tips:
1.)Beat game once
2.)Find all sabu statues
3.)Equip hasabi and mami charm and re-enter final boss room