New Game Plus
When beating the game for the first time, you will achieve Ending A. Save your data to begin a second playthrough with all of your gear and progression intact. Load up this save to start the subsequent playthrough for Ending B.
Once you've defeated the game 3 times, save the game. This new save file will let you access Chapter Select and Debug. From Chapter Select you can launch any part of the story you have unlocked. The menu will now show you your progression. Side Quest progression will carry over from playthrough to playthrough so you don't need to redo them. Debug Room lets you fight enemies in a room to practice combat.
It is important to mention that because any quests not started or completed during the first three playthroughs, A, B, & C, D, or E, if one wishes to play them over again it is possible to save them all for completion in their entirety. Therefore, if you decide to play only the main story, all the quests, un-opened chests, unfound items and unpurchased weapons will be there if you play the game again from the beginning of your game after the third playthrough. This is important if you want to play over again with the weapons and pods at the level you left them at the point when the game ended the third time. So, as long as one retains a "master copy" of the progression such a game, it is possible to play all of the quests again from that particular saved game. This applies to chapter select play of such a game as well. However, played quests may not be reset in any other manner unless a new game is begun from the very start.