The Bonus Area is located behind a secret wall. Search the upper-left walls of the large cave area in the Destroyed Junction. It has a 7-digit password which happen to be the first seven numbers in the famous Fibonacci Sequence.
Inside can be found three enemies (Baron, Revanant, Apollyon). The floor is covered with Berserker and Soul Sphere power-ups, a dog collar, a Flak Jacket, and large amounts of ammo for every gun.
At the title screen or while the game is paused slowly press 3666.
Then select “Cheats” option
If you go through the game and collect all the super secret password clues, you will be able to enter the super secret room which is in level 6.