Each Main Path and Timeline level have a Bonus area, which can be accessed by finding and standing upon the platform with a yellow question mark on it.
- Each Bonus area contains a set number of Wumpa and Crates within that area to collect.
- Features a short puzzle-like sequence the player must solve in order to break all the Crates and collect all Wumpa in the Bonus area.
- When you die within a Bonus area, it will not deplete a life (in Retro), and you will respawn at the spot in the level just before entering the Bonus area.
Also, there are four secret Colored Gems hidden throughout the game. When one of these is collected, a special Bonus area becomes unlocked in another level.