most probably this page should be depublished and removed as outdated. please, see Finales and Endgame page for more details
There are three endings to the game. Proceeding to the next ending will be more difficult that the previous. They require secrets, and special items to be found. Currently, the first ending and assumptions on the second and third will be included. Lastly, the developer did state in an interview that there are three endings. Though, there could be more ; ).
This ending is achieved by simply beating the game with no special items. By beating, I mean getting to the final Library stage. To do this, you must obtain all three souls found throughout the levels, place them on their respective altars, and enter the door that is unlocked. You will now be climbing UP rather than pushing your way downwards. This creates an environment that is harder to navigate. On each stage of the library you will find a book describing what is currently going on. You will read about a binding ritual that can be performed in different manners. The Bad Ending results in you being the eternal protector of the Library to close off the world from the evils. Some have escaped though, and you are forever stuck to keep them from running rampant once again.
I have not yet achieved this ending, when I do this will be updated. For now, this is all assumptions. I believe the good ending will require no more than the religious symbol. This will force you to play without an amulet or compass starting on Dagon level 2. There will be a book symbol that will have no access. The player must either find dynamite or a destruction amulet to reach this area. There will be a Dusty Book inside. Once you enter the Shadow World, you will see black tiles lighted with purple. Artifacts will be all over the ground, though there are only 2 rooms so don't expect a lot, and a Religious Symbol item at the end. There are no creatures here. I believe the religious symbol will also have an effect that makes the game harder. I think it attracts more cultists (please confirm!). You should unlock the next ending by completing the game with this item on your person. It obviously creates a much more difficult envrionment. I believe the key difference in this ending will be that the creatures will not have been left lose on the world at all, though you will likelys till be the eternal protector.
This ending should be even more dangerous than the Good. There is likely another secret room on Nyarlathotep or R'lyeah. I'm under the assumption the item will take the place of a weapon. Why a weapon? Because if you have to choose between a knife, a tripwire gun, or a revolver which would you take? The choice is easy with two slots, with only one slot you're you'll effectively be able to disarm yourself at times. The final reason why I believe it will take the weapon slot is this, while in the second library room one of the books described having a Damsel I believe. It would make littler since for you to carry around another person and not have them take up an item slot. The increase in difficulty, and the hints from the books, would make me assume that this is the path to the great ending. Along with the religious symbol. Though, it's possible that this may be achieved by gameplay style as well if these are neccesary ingredients for the Good ending rather than the Great.