The Time Gears are artefacts of great importance in Pokémon Mystery Dungeon: Explorers of Time & Explorers of Darkness and Pokémon Mystery Dungeon: Explorers of Sky.
The Time Gears help keep control of the flow of time in the Pokémon world. Even the most hardened criminals know not to disturb the Time Gears, lest the proper flow of time be disrupted in that general area. However, in the beginning of the events of Explorers of Darkness, Time, and Sky, a mysterious thief starts to steal them over the course of the storyline, causing time in those areas to stand still. All but two Time Gears are guarded by the lake trio, and all but one Time Gear is guarded in any way. There is also a sixth time gear present in the Partner's story and in the start screen on Explorers of Darkness shown in a volcano setting. However, this sixth time gear is never brought up again in the games, and it is unknown if it actually exists.
The thief is found to be Grovyle, who was from the future, and the player character eventually brings him to justice. The stolen Time Gears are then returned to their respective areas. However, it is then revealed that Grovyle stole the Time Gears to prevent an even greater catastrophe: the paralysis of the planet, and that Dusknoir, a famous explorer who was presented as a hero at first was the real enemy and a servant of Primal Dialga, the main villain of the first storyline, in the future. Grovyle came back from the future with the player character to stop the paralysis of the planet. The frozen time would be only in effect temporarily until the Time Gears were placed in Temporal Tower, Dialga's domain, where the flow of time would be fixed permanently. The player character then decides to help Grovyle collect the Time Gears again. The player character and his partner go to the guild and tell the guild members the whole story, and that Grovyle should be allowed to take the Time Gears.
When the player character and Grovyle go to Treeshroud Forest to take the first Time Gear again, time has already frozen, further proof of Grovyle's story. Acting fast, Grovyle obtains the rest of the Time Gears and the party goes to the Hidden Land, and from there, Temporal Tower. Grovyle throws himself and Dusknoir, their pursuer, into a portal going to the future, while he entrusts the five Time Gears to the player character in order to prevent history from repeating itself. Together, the player character and partner place the Time Gears in the slots at the top of the tower, after defeating Primal Dialga, and prevent a future of darkness. The story of Grovyle and Dusknoir is then continued in the Special Episode In the Future of Darkness. It is also later revealed that Darkrai was behind the events of this story in the first place.