From your starting position, turn right and blast a darker-colored section on the wall to reveal a Super Health and Serious Damage.
At the end of the second corridor, you can see Groovy Gregory hanging out from one of the windows of a tower. Shoot him to spawn a Serious Damage.
In the middle of the third corridor, on the wall at the left, shoot a darker colored section of it to reveal a teleport to a secret pumpkin field. Watch out for Static Cannons placed there, and do not move out of the path, unless you want to spawn some extremely small Cucurbitos.
(HD-only) in the fifth corridor, on the right wall where Beheaded Kamikazes spawn, at the base of a pillar is a darker colored section. Shoot it with any weapon to reveal some secret items.
In the sixth corridor, on the right side of the wall is another darker section. Blast it to reveal a teleport to an embryo museum. Picking up any power-ups there will spawn two Highlander Aludran Reptiloids: one on the left and one on the right.
At the end of the sixth corridor and at the start of the seventh and final one, at the tower on the left there is a Scythian Witch-Harpy mooning at the player from a window. Shoot her with the sniper rifle or rockets to spawn an Invulnerability power-up.
In the final battle, after approximately 85-90 seconds, a small section on the right side of the wall will open, revealing a secret Super Health.
If the player's health is low enough and the player is too close to Mordekai The Summoner when he dies and explodes, the explosion will kill the player; the game will however still count as cleared with a sound of applause, with the Croteam Bigheads appearing to mourn the death of Sam.
In the embryo museum, there appears to be Ugh-Zan III, or at least a clone of him, inside a large tube with green liquid.