Prodigy Special Edition secrets by Stefan Schwoon.

Start map:
1. To reach nightmare mode, walk to the area of the fourth map (Sombre Citadel). Halfway up the spiral staircase, there's a stone with a rune on it. Shoot it and run back down - at the feet of the stairs the entrance to Nightmare has opened.
2. To reach the secret level, again walk to Sombre Citadel. Walk up the stairs all the way this time. When you're about to enter the teleport, the game will say "The secret level entrance is near." Turn around. On your left, there's a window with one rune on each side. Shoot both. Take note of their appearance (slightly S-shaped). Run back to the central level selection hub. There's an ornament with five different runes on the ceiling. Shoot the one that looks the same as the previous runes, and the secret level entrance will open.

Arrival (p_se_1):
1. After pressing the first switch, enter the water area on the left. Climb up the stairs. You can jump to a narrow ledge over the gate that's too heavy to lift. Touching the elevated brown stone there gives access to a quad on the far end of the level (in the area with rocks and the shell box).

Ebony Shrine (p_se_2):
1. There's a lift in the area above the Scienide Switch. Behind the lift is a yellow armor.
2. Ride up said lift. The keystone of the archway leading out to the central open area has a different rune. Shooting it reveals a secret down left in the acid.

Venom (p_se_3):
[Just had to mention it: This is one of the best maps, if not the best, I've *ever* seen! One of my all-time favourites!]
1. From the start, go left to the grenade launcher. High above the grenade launcher is a walkway (you can't get up to the walkway from below, but let's assume you can. Follow the walkway to the left. It leads to the large fortress-like area. Somewhere along the route is a recess in the right wall. Shoot it, get the red armor and complete the monster count :)
2. When you emerge from the previous secret, turn left and find the shootable button high up in a niche.
3. After the second secret, turn left, walk up the stairs and enter the guard tower. There are suspicious ornaments on the walls. The right one has a skull in the middle. Shoot it, leave the room, turn left and enter the next room on the left side. Part of the floor will have moved, allowing you access to a health box and a quad.
4. From the belfry area, a narrow hallway leads to another area with a pool of water. The side opposite the entrance has a sloped roof, and you can see an entrance in the storey above the roof. Jump there from the lift that crosses the water.

Sombre Citadel (p_se_4):
1. At the start, follow the right road. You will come into a small hallway with lava on the right. Under the stairs, an armor is hidden.
2. In the same room, look at the wall behind the lava. In the middle of it, the texture is darker than normal. Shoot it and jump into the lava. You will fall into a secret area and get a quad.

No secrets in p_se_3b and p_se_xxx.