Time has gone awry, and the Doctor calls upon the player to help him gather his most loyal companions, battle his deadliest foes, and help to set the timelines back on course. The player chooses a team of characters, selects a mission, then conducts a series of gem-matching battles to earn experience and items, unlock new playable characters, and progress the storyline.
Missions are grouped into "seasons", working backward from season 7 (i.e., when season 7 is complete, the player moves on to season 6). Each season of the game represents a warped version of events from a given season of the revived TV show (2005-present), where one or more antagonists have changed established events to serve their own ends.
Each character is associated with a gem color; completing a match of three or more gems results in an attack from that character, and a charge to his or her unique special move. Those moves may include a powerful extra attack, healing the party, stunning one or more enemies, or other status effects. Matching pink gems restores some of the party's energy, which enemy attacks continually drain. Unlike many gem-matching games, for a short time the player is free to drag a given gem anywhere on the play field, displacing other gems in the process and allowing the player to carefully set up and execute large and elaborate combos.
As characters earn experience they move up in level, allowing the player to assign limited bonuses to their attack, healing, or base HP statistics. Every ten levels, a character's experience is capped. To break the cap and allow further development, the player needs to find (or, optionally, purchase) a combination of special items. Players may also purchase extra characters or costumes from the store -- although most are also available in the normal course of play.