The Deep Power Stones were a pair of legendary crystals. Combined in one way they granted extraordinary power, whereas combined another way they could cause mass destruction. They were hidden by the royal family.
Eventually, Robotnik managed to translate the scrolls that told where the stones were. The Freedom Fighters set out to stop Robotnik from getting them, but he nevertheless successfully obtained the first stone. However, thanks to a plan by Tails, they were able to prevent him from finding the second stone by finding it first and then convincing Robotnik that they had destroyed it. In fact, they had destroyed a fake, and brought the real stone with them back to Knothole.
Later, when all seemed hopeless, Sonic stole Robotnik's stone. He and Sally then called upon the energy imbued in the stones to defeat the Doomsday Project. Originally, they intended to unleash the power of destruction contained in the two stones, but later combined them in the other formation to grant them super abilities. It was revealed that physical contact between users of the stones produced further energy, as demonstrated by first a high-five, and later a kiss, between Sonic and Sally.
The Deep Power Stones are also known to have the same energy found in the Power Rings, but 10,000 times more powerful.