[1] Although the prequel/sequel to Mario and Luigi: Superstar Saga, the game's plot is completely unrelated to that of its predecessor with more emphasis on the time-traveling theme, which involves the protagonists traveling in between the past and present of the Mushroom Kingdom.

[3] The gameplay centers on the co-operation between the quartet, who must use their specific qualities and skills to solve puzzles to progress through and features multiple role-playing game elements, but with a turn-based battle system focused on timing accuracy.

Mario and Luigi: Partners in Time was critically acclaimed by the media, gaining an aggregate score of 86 from Metacritic.

[9][10] Such instances form multiple puzzles in the game, in which items or switches can be only be accessed by use of the babies' specific qualities.

[11] These actions, such as the "Toadsworth Twist" (more commonly known as the "Spin Jump") that allows the older brothers to twirl through the air, are required to advance through the game and solve the various puzzles.

The game retains many of the RPG aspects present in its predecessor, including the interaction with non-player characters, which is required to advance the plot and gameplay.

Each character's progress is measured by experience points, which are needed to "level up", a process by which battle-related statistical fields such as speed and power are boosted.

[10][12] The battle system is similar to its predecessor's, with the effectiveness of an attack dependent on the timing accuracy of separate actions.

Baby Bowser harasses the quartet frequently during their journey by stealing their Cobalt Star shards, and later attacking the group with his older self.

[16] Kamek the Magikoopa, Petey Piranha and Fawful, an antagonist from Mario & Luigi: Superstar Saga, appear in the game as well.

AlphaDream also introduced Stuffwell, a talking briefcase created by E. Gadd who gives the player and brothers advice regarding items and accessories, which he stores.

[6][7] IGN's Craig Harris commended the game's comic style, stating "much of the charm from Mario & Luigi comes from the focus on humor that's bizarre and out there".

Despite this, GameSpot's Ricardo Torres stated that "The self-referential humor that gave the original game its bite isn't as prevalent".

[10] Nintendo World Report''s Jonathan Metts praised the game for returning to the traditional Mushroom Kingdom setting, claiming it led to more distinctive character and plot elements.

[2] While appreciating Partners in Time's use of humour, RPGamer's Derek Cavin criticised the game's plot, describing it as "a basic story that doesn't develop as much as it could have".

[2] IGN noted that "Partners in Time's quest starts out a little too easy", although they acknowledged that the game became increasingly difficult as it progressed.

GameSpot appreciated the "added flair" in animation gained by the DS, although the perspective made such things as hitting blocks and countering attack "trickier than it should be".