Aquatic Base

Aquatic Base is a level in Sonic '06. The area is a high-tech Soleannan research facility, hidden beneath the waters of Kingdom Valley. It is here that the Duke of Soleanna was conducting time-travel experiments on the Flame of Hope.

Aquatic Base was partially destroyed in the explosion that curtailed the Solaris Project (an event which also created Iblis and Mephiles). Along with the royal palace in Kingdom Valley, it was subsequently abandoned. Some years later, Doctor Robotnik clandestinely moved into the facility, using it as a secret base and hanger for his Egg Carrier.

Sonic's story
The Aquatic Base is the final level for Sonic in his story. After going back through a rift opened in time from him and Silver colliding two chaos emeralds together, Sonic goes through the abandoned factory in order to reach the end of it and land on Eggman's aircraft that is about to take off. Although it isn't explained how, Tails and Knuckles are there as well and are playable during certain parts of the level.

Shadow's story
The Aqautic base level took place in Shadow's story at the same time it did in Silver's. After the two hedgehogs ended a fight with neither of them being the victor, a rift in time was opened up with chaos control. It was a portal that sent them into the past. Shadow and Silver, both determined to find answers, jumped into the portal and reached the Soleanna laboratory to witness the Duke of Soleanna and his scientists as they experimented on Solaris. Unfortunately the project was a failure and an explosion took place before they could reach the area. Upon inspecting the wreckage, they saw Solaris split apart into the original forms of Iblis and Mephiles. Silver was set to persue Iblis while Shadow, after being handed the scepter of darkness from a barely alive Duke, set his sights on Mephiles. You proceed through the level and are able to play as Silver at one point.

Silver's story
The Aqautic base level took place in Silver's story at the same time it did in Shadow's. After the two hedgehogs ended a fight with neither of them being the victor, a rift in time was opened up with chaos control. It was a portal that sent them into the past. Shadow and Silver, both determined to find answers, jumped into the portal and reached the Soleanna laboratory to witness the Duke of Soleanna and his scientists as they experimented on Solaris. Unfortunately the project was a failure and an explosion took place before they could reach the area. Upon inspecting the wreckage, they saw Solaris split apart into the original forms of Iblis and Mephiles. Silver was set to persue Iblis while Shadow, after being handed the scepter of darkness from a barely alive Duke, set his sights on Mephiles. You proceed through the level and are able to play as Shadow at one point.

Triva

 * It isn't at all explained how but during the course of Shadow and Silver's levels the enemies you fight are all Eggman robots despite the fact that they were exploring the Soleanna laboratory 10 years before the current storyline. Eggman's robots should not have been anywhere near the lab at this time.
 * No hint of Tails and Knuckles was there before or after the Aquatic Base level which obviously means that there was no reason for them to have been there story wise.