Upon completing Pandora's Tower, you have the ability to play through the game again from certain Chapters, or points in the game. There are 4 Chapters:
- Start: Against the Odds
- Tw. 6: Still Feel the Same
- Tw. 11: Hope Survives
- Tw. 13: To the Endings
In each chapter, there are a number of Towers. Chapter 1, Against the Odds, features the first five Towers. The next five Towers, which are unlocked all at once upon completing Chapter 1, are part of Chapter 2, Still Feel the Same. The third Chapter, Hope Survives, consists solely of the Blacklight Barbican, the Dawn and Dusk Towers. The final Chapter, To the Endings, is the section in which you will fight the final boss in the game. Depending on your Affinity level, you may go to the Centrum tower; otherwise, you will go into the Courtyard to fight a weakened version of it. Note that if your Affinity level is low enough, you will not be able to access this Chapter: you will achieve the D Ending, which occurs after the 9th Master flesh is eaten by Elena.