The Magic Stone (also called the Pendant Stone) is an item created by the ancient Pendant civilization to lead its owner to the soul of the legendary Phoenix. The catch is that only someone of the ancient Tochikan bloodline can operate it.
In the anime series, one such person is Holly. She uses the stone to guide the Searchers to where they think the Phoenix's mystery disc is hidden, but what they don't know is that the stone instead leads them to five monsters who possess pieces of Suzaku's soul (Tiger, Mocchi, Suezo, Hare, and Golem).
Moo also steals and misuses the stone in order to find where his ancient body is frozen, and since he possesses Holly's Father's body, he also has access to the ancient bloodline. This allows him to recover his full power and withstand the damage done to his body by the sunlight.
In the third season, the stone is the key to unlock Moo’s Mystery Disk and release Holly's father from the evil spirit within at a special shrine. The stone amplifies Holly's willpower to save her father and restore him but without his memories. Later, Durahan and his goons use the stone to unlock Moo's spirit from the disc in order to become the most powerful monster but are consumed by the evil spirit and transformed into Ruby Knight.
The stone was originally created to house part of Suzaku's soul, which is why it shows a firebird within it when it is activated. When the user concentrates on what they wish to find, the stone glows yellow and the firebird points the way to the location like a compass. Holly only understands the power of the stone on the surface, and thus has a hard time unlocking its potential as more than just a searching device.
The Magic Stone (like the other Gaea Stones) can also be used as a power source, much like battery or nuclear reactor. The Pendant scientists who helped create the stones also used it to power quite a bit of their weapons technology. The stone projects an energy field which reactivates any of the machinery within a short distance.
Finally, the stone is also important in drawing out the last piece of Suzaku's soul, which was shattered into five Monster Orbs and hidden within The Searchers' monsters. The stone fuses the pieces back together.
Thus it is said: "The stone shall choose its owner, and only the chosen one shall gain its power."
-"Ancient Stone, Part 4" MR4