Get to the top of the stairs near the great pyramid. Instead of heading up the ramp, take a left and walk across the desert sand. Take a left and head toward the building with a smaller pyramidal shaped roof. Jump onto the roof and head to the top to reach the secret, and get an atomic health pickup.
Drop down from this same building and walk up to dead Serious Sam.
As soon as you enter the pyramid, head up the stairs and look right at the pillars. Open the hieroglyphic picture to find a box of pipebombs.
In the fire room with the lava, destroy the crack in the wall and walk through.
In the water room, find the crack in the wall and walk through.
At the end of the level, after destroying both reactors, head back to the switch that revealed these reactors. Turn to the wall opposite this switch, crouch, and walk forward to get the secret, and gain access to the secret level exit.