To reach the Super Secret shrine you must jump from the pillar to the ledge at area 9. Here a secret door can be opened. Beware of the fire ball trap within! Best tactic is to stand in the doorway until the door lowers, hits you on the head and reopens. Quickly step into the room and back out into the doorway. This door is quite thick so the doorway is plenty deep enough to shield you from the fireballs. You can then enter the room to see a portrait of one of the games developers. Clicking the picture will reveal a hidden message.

There is also a secret room that can be seen on the map north of area 8. There seems to be no way to activate this door from the outside. Inside there is a chainsaw. This seems a rather meager prize for such a differcult secret to figure out. So maybe it's a forgotten room from the original game which the developers decided to leave out. Neither the room nor the Chainsaw seem to be tagged as a secret and this room can only be enter by using the 'no clip' mode as far as I'm aware.
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Completing the level all the way up to the point where you enter the last room and kill the lost souls will open a secret room behind the bars at area 4 which contains a timer switch. This switch will open the door to the super secret shrine over near area 2. This might sound simple enough but trust me, it's very difficult to get right so here are a few tips.

First you need to hit the switch whilst in the process of running backwards onto the lift. Don't bother spinning around to face the lift. When the lift has risen, back yourself out and around to area 5. Your job then is to navigate yourself around area 5 as quickly as possible. To do this you must perform what is know as 'Strafe Running'. This is done by turning 45 degrees from the direction you are actually running. Best to turn on the map and practice this until you're familiar with the technique. Strafe running increases your maximum running speed and you will need every bit of it to reach the shrine door before it closes. Because this technique requires you to face in a different direction to the way you are heading you will find this easier with the map as your guide. With the map on you will be able to see how your speed increases when you strafe run correctly.

Also note that this secret door stays open longer the first time the switch is activated. After that the time delay is reduced so you only have one chance to reach the door. Save your game before activating the switch. Upon entering the secret shrine beware of the fireball trap to your left. This trap is truely deadly as it unleashes so many fireballs. To avoid being hit you must step forwards into the room. As you near the portrait you will hear the trap activate. This is your cue to run back to the door as fast as possible. Stay close to the left wall and you will be protected from the fireballs.
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This was a very tricky secret to find and is very difficult to achieve. First you will note a trip line at area 11 on the map. Passing over this line towards area 10 will cause a hidden wall switch to appear at area 12. This is the back of the Arachnotron pen in the blue key room. This pen is completely blacked out so it is impossible to see the switch from the blue key room. The trick to this secret is to run up the arrow trap pathway towards area 10 until you hear a mechanical sound, at which point you must spin round and head towards the teleport directly in front of you. This will take you back to the start room where, you must head back into the fireball room and to the teleport on the right which will take you to the blue key room.

Now things get really tricky... As you teleport in, take a single step forwards, spin around, hit the hidden switch you can't even see with the ChainGun, then step back onto the teleporter. If you managed to hit the switch a secret door at area 13 will have opened allowing you to enter the secret teleport room. The time the door remains open is very short indeed. You pretty much have to hit the switch whilst stepping back onto the teleporter if you wish to make it through the secret door before it closes. Aim for the top right corner area of the Arachnotron pen as this is where the switch can be found. Let off a quick burst of the ChainGun as you step off and onto the teleporter. If you are lucky you'll hit it.

As with the previous secret, I've found that the time delays are more generous the first time the switch is activated. The teleporter at area 13 will take you to area 14 beyond which is the Shrine. Beware as another fireball trap awaits you. To avoid being hit, open the door and side step quickly to your right. Along with a portrait and message there is another teleporter that takes you back to the start room. When you attempt this super secret it will become clear why this level has a respawning soulsphere in the blue key room.
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The solution to this super secret is as yet incomplete. But here's some insight into unlocking it. You will note on the map that the yellow key area holds three secret rooms that don't show on the map. I have labeled these A,B,C. Room 'A' is opened by a secret wall switch in the corner of the secret room near area 11. Room 'B' is opened by the switch in room 'A'. This room contains an AutoMap and also a trip line that will open room 'C'. Room 'C' contains a normal switch which as yet has an unknown purpose. The door of room 'A' seems to suffer from a glitch. When opened by the switch I mentioned it still appears to be closed. You can however still jump through it. This door has a generous time limit so entering it isn't that much of a problem. If you get from the secret switch to room 'A' quickly it won't have actually opened and takes a further second or two before you can pass through it. This just adds to the confusion. However the whole 'A to B to C' sequence seems to be on a strict time limit, so failure to enter room 'A' quickly will mean room 'C' will be closed by the time you get there. Futhermore it seems once you have picked up the AutoMap and/or tripped the line in room 'B' you only get one attempt to get to room 'C'. After successfully completing the sequence, I've have attempted many times to reopen room 'C' with no luck. Even if you don't activate the switch within room 'C' it seems once you have entered room 'B' and picked up the map you have one chance to get there. Room 'B' is also tricky to enter as you have to use the Jump but time it just right. Jump too late and you will be too high, bumping yourself on the wall and falling to the floor. You cannot enter room 'B' by simply running across the gap. It is best to save your game when you enter the secret room near area 11 so that you can retry this over and over till you get it right.

There are also two super secret rooms in area 4 which are the actual shrine. As of yet I do not know how to open them.
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