This stage is known to be Eggman's secret base, and also it used to be a Soleanna research facility 10 years ago. Similar to G.U.N. Fortress from Shadow the Hedgehog. Aquatic Base is a heavily armed Underwater base with windows showing water creatures swimming around. The base is made of metal and has badniks that were shown in Kingdom Valley and Crisis City guarding the area. It also has homage to the Scrap Brain zone "Sonic the Hedgehog", The Panic Puppet zone from "Sonic 3D Blast", and the final Egg from "Sonic Adventure".
- Sonic's Story (Final Stage)
- After realizing time has run out and after witnessing a terrible event, Sonic enlists the help of Silver to go back in time to save Elise from a horrible fate by sneaking on board Dr. Eggman's battleship.
- Boss: Egg Wyvern
- Shadow's Story (7th Stage)
- In an attempt to uncover the truth about Mephiles, Shadow and Silver decide to travel 10 years into the past, when this world was still a research lab for the Duke.
- Silver's Story (7th Stage)
- Silver accidentally induces a Chaos Control, which opens a time portal while he's fighting against Shadow. They decide to uncover the truth about Mephiles and Iblis and travel back 10 years ago when they were released.