As of version 3.0.9, to access Proto Palace Zone, the player must first access the Level Select (start the game in "No Save Mode", tap the S-E-G-A letters when the Sega logo appears and hold two fingers at the title screen), input the Debug Mode code in the Sound Test (01, 09, 09, 02, 01, 01, 02, 04) and then must input an exclusive code in the Sound Test as follows: 03, 03, 03, 0B, 10, 10, 10, 04. (A Ring sound will play if successful.) Then the player selects Hidden Palace Zone.
While the layout still remains unchanged from the prototype versions, changes were still made, such as platforms being added over the mid-level pit and newly functioning water slides. The Redzbadniks also have their original behaviour restored. The infamous TailsMonitor is also present which still functions as a regular 1-Up regardless of the character(s) who breaks it. If the player jumps on the "Master Emerald"-like object, he/she will be warped back to the Level Select. The background music used for Proto Palace Zone is the unused Track #10.
If the player dies in this Zone by any means, the game will not load this Zone and will load Hidden Palace Zone instead.