Infinity Stones

The Infinity Stones are twelve powerful gemstones that are one with the fabric of the universe. They are a key element in the last two sagas of Freedom Fighters NEO (the Lord Vortech Saga and the Mephiles Saga). They can control Soul, Mind, Power, Space, Time and Reality, and are said to be more powerful than the Chaos Emeralds, and altogether they're even stronger than the Master Emerald. Mastery over one of the things the Stones control facilitates the use of another Stone.

List of stones

 * Soul Stone, powered by the user's mastery of reality. Observe, attack or even steal a being's soul or spirit. Also used to revert individuals to their natural state. Currently, it's located in the Null Space.
 * Mind Stone, aka the Precioustone, powered by the user's mastery of soul. Near-limitless psionic/psychic abilities including empathy, telepathy, and telekinesis. Current guardian: Emerl.
 * Power Stone, aka the Deep Power Stones, powered by the user's mastery of mind. Increases strength and durability, enhances virtually any known superhuman ability, energy manipulation. It can enhance one's speed, as seen when Sonic and Sally destroy Robo-Robotnik's Doomsday Weapon, as well as trashing Robotropolis. Current guardians: the House of Hedgeacorn.
 * Space Stone, located in Vorton World (an area of the Null Space), powered by the user's mastery of power. Allows travel through space, mostly through teleportation. Able to interfere with the motion of other objects.
 * The seven Time Stones, originating from Miracle Planet, powered by the user's mastery of space. Allows for time travel, stop, slow down or speed up flow of time, accelerate or slow down aging, see into the past and future, and bend time to the user’s will. Six Time Stones are well hidden into The Brotherhood of Metallix's Interstellar Amusement Park; the seventh one was entrusted to Time Man.
 * Reality Stone, aka the Phantom Ruby, powered by the user's mastery of time. Allows to alter reality to what one wanted or break the laws of reality, logic and physics. Able to resurrect the dead, distort reality around someone so it was incomprehensible, or other things that would normally be impossible. More powerful uses allowed one to create any type of alternate reality one wished. According to Mephiles, this is the most powerful of the stones. Current guardian: Emperor Metallix.

Lord Vortech Saga
When it is revealed that Lord Vortech was a pawn in Mephiles' plan to destroy Metallix, Mephiles put the Space Stone in his Infinity Gauntlet, and used it to bring the rest of the Stones to him. Mephiles easily got his hands onto the Soul Stone and Deep Power Stones, but the guardians of the Mind, Time and an alternate reality version of the Reality Stones, Emerl, Time Man and a past version of Infinite, respectively, refused to give up without a fight. Unfortunately, Mephiles beat all three of them, seizing all Infinity Stones. He attempts to destroy half of the universe with the Stones, but fails to kill any of the Freedom Fighters, due to a miscalculation: Emperor Metallix was the true guardian of the Reality Stone. This allowed Metallix to prevent any Freedom Fighter from turning to dust (with a heartwarming/tearjerking moment between X and his children), but many Koopa Troop members were lost, as well as a few thousand Metallix Troopers.

Mephiles Saga
Metallix attempts to take back the Stones, but unfortunately, Mephiles destroyed them to ensure his victory. Metallix, in rage, crushes Mephiles' head. Then, Dr. Koopa decides that the best way to undo what Mephiles did is time travel. They did time travel and took alternate reality versions of all Infinity Stones, including the Reality Stone, in order to keep Mephiles in the dark about Metallix's Phantom Ruby, in case his past self decided to time travel himself. Unfortunately, present Mephiles wasn't dead. However, Metallix, due to being the only one aside Bowser and Shadow who could handle the gamma radiations of the Infinity Stones, modified his gauntlet so it had openable slots for the Stones and undid the damage Mephiles did before Mephiles could try anything.

Mephiles believes he'd rather destroy the whole multiverse with all with Metallix and all the Freedom Fighters, and seizes the Infinity Stones. Rock, in an act of desperation, clinged to Mephiles' Infinity Gauntlet. Mephiles did toss Rock aside, and planned to snap his fingers, saying the words "I AM INEVITABLE!", but when he snapped his fingers, nothing happened. It turned out that, in his moment of desperation, Rock managed to steal the Stones from the gauntlet and used them on himself to achieve Dr. Light's dream of everlasting peace. Saying the words: "And I... am... Mega Man!", Rock snapped his fingers, fully killing Mephiles. Mephiles, knowing that Rock can't handle the energy of the Infinity Stones, stated that, if this was truly the day for him to die, he'll at last take Rock with him, until he saw Rock getting up, all of his injuries healed. Mephiles then realizes that Metallix was the one healing Rock, and figures out then that Metallix was the true guardian of the Reality Stone.

Metallix then returned all of the past Infinity Stones to their rightful time period. However, Mephiles' death allowed the Reality Stone to recreate the other Infinity Stones.

Trivia

 * The Infinity Stones are based on the gems of the same name from the Marvel Cinematic Universe.