In the very first room where you get your first weapons, you may opt to retrieve and trade them for an elixir. However, the game will not advance unless you have weapons, so they will reappear. Continue to trade those respawning weapons for elixirs until you tire of the exercise.
If you enter a room that you had cleared out once before there may be enemies inside of it. If you see enemies when you enter a room, go back the way you entered and then enter the room again. The enemies will be gone.
When you first begin the game and are in the room where you first get a weapon and learn how to turn items into Elixir, turn both weapons that you get into Elixir. Since the programmers didn't want you to have to start off without a weapon, both weapons will re-appear. Collect both weapons again and then turn both of them into Elixir again. Repeat the process as long as you want, and since Elixir is what you use to power up you can make your character as powerful as you want right from the start of the game.
Once you leave the starting room the weapons will no longer keep re-appearing.
Beat the game twice to get the true ending with a cinematic cut scene.
Lycaon - Beat Lycaon in the Tower
Mars - Beat Mars in the Tower
Alkmaion - defeat Alkmaion and save
Briareos - defeat Briareos and save
Statius - Defeat in lvl 7 boss fight
Gryphus - Defeat in lvl 8 boss fight
Minos - defeat Minos and save
Sphinx - defeat Sphinx and save
Deucalion-A - Finish the game twice
Deucalion-B - Finish the game twice
Type01 - Save at least once
A.D.A.M - Save at least once
Others-A - save at least once
Others-B - save at least once