Sequel to the Game Boy Advance game Mario & Luigi: Superstar Saga, Partners in Time features the series heroes, Mario and Luigi, with the addition of their baby forms (Baby Mario and Baby Luigi). This time around, the protagonists need to save Princess Peach, who has been abducted by the Shroobs, an alien race.
The story unfolds as Professor Elvin Gadd finishes his most recent invention a Time Machine which gets its energy from the Cobalt Star. Princess peach filled with enthusiasm jumps in and travels to the past, at her arrival she notices the Mushroom Kingdom is under the attack of the Shroobs. She is abducted and the time machine returns with a member of the Shroobs.
On the journey to save Peach Mario and Luigi run into their younger counterparts; Baby Mario and Baby Luigi. All four agree to search for the crystal fragments, which are shards of the original Cobalt Star which blew apart when Peach traveled to the past.
The gameplay in Mario and Luigi: Partners in Time is very similar to that of the original game, Mario and Luigi: Superstar Saga. Players navigate basic platforming challenges on the overworld with both characters and fight enemies in turn-based form. However, this game advances this system by adding two more playable characters, Baby Mario and Baby Luigi. These two infants spend the majority of the game riding on the shoulders of their older selves. Certain sections of the game require the babies to leave the adults and wander alone, often to find a switch hidden in an area too small for the elder pair. Additionally, these two aid in combat as the only bearers of hammers.
In the original game, Mario and Luigi earned hammers early on. In this game, Baby Mario and Baby Luigi earn hammers instead. As such, hammer attacks can only be used if the Babies are available in combat. Another change to the system is the Bros Attack Item. This system replaces the Bros Attack system seen in the previous game with a new system. This system uses an item in your inventory to attack an opponent.
Generally, the power of an item is increased by responding to onscreen events. For instance, with a green shell Mario and Luigi's respective buttons must be tapped whenever the shell is close enough to kick, otherwise the attack ends. Additionally, if a baby is riding the shell it is possible to deal additional damage by tapping the baby's button as the shell hits the target. This system varies from item to item. Also, Mario and Luigi are able to perform standard jump attack, the game introduces a feature to add a critical strike on to your attack by tapping the button corresponding to the character, Mario being A and Luigi being B. With Baby Mario and Baby Luigi on the brothers' shoulders, you are also able to attack with them by hitting the corresponding button, X for Baby Mario and Y for Baby Luigi, before you hit the enemy resulting in four attacks per turn, if successfully landed.
Some new moves appear in Mario and Luigi: Partners in Time. These moves are useful in the platforming sequences of the game, as navigating most environments would be impossible otherwise. These moves are learned as you progress through the game, primarily from the Toadsworths of past and present.
- Spin Jump -This move allows Mario and Luigi to spin. This spin gives them extra distance when they jump. It also triggers the Baby Spin.
- Ball - This move allows Mario and Luigi to roll into a ball. This spin allows them to move with great spin. It also triggers the Baby Cakes.
- Hammer - This move makes Baby Mario use his hammer.
- Drill - This move allows Baby Mario and Baby Luigi to tunnel underground. This allows them to move under certain objects, and also allows them to dig beans.
- Baby Spin - This moves allows the babies to move great distances. By using the Spin Jump and touching the babies while spinning, the babies receive a lift and corkscrew until they hit the ground. This gives greater distance than the spin jump, however, the babies lose height as they go.
- Baby Cakes - This move crushes the babies into little pancakes. This is triggered by rolling over the babies while in ball form. While flat, the babies have great air resistance and can be lifted by fans. The can also move into thin spaces.
- Water Spit - At certain times, the babies find a small spring. Baby Mario can drink from this spring, and then spit up the water when hit by Baby Luigi's hammer. This is useful when trapped by fire, and can also be used to hit certain items out of the sky.
The Bros. Items are used for attack. Each is useful depending on the circumstances. All of these items require at least one Mario and one Luigi, and some require all four brothers.
- Green Shells - These items are volleyed between Mario and Luigi. To use, one throws the shell. It automatically hits the target. It then bounces towards the other brother. The other brother must then hit his button so that the shell will bounce back. It keeps going until the player misses a button press or the enemy dies. If a baby is present, the baby's button can be hit on contact with the target to do extra damage.
- Red shells - Same as green shells, but more powerful. Also, if the target dies, the shell advances an enemy and you can keep dealing damage.
- Bros. Flowers - These items spawn a fireball that alternates between the brothers. The player mashes the button of the brother with the power of the fireball to throw fireballs at the enemies. Potentially deals the burning status effect.
- Ice Flowers - Same as Bros. Flowers, but deals ice damage. Potentially deals a downgrade status effect.
- Smash Eggs - These items are essentially vertical versions of green shells. An egg is thrown in the air, and will come down on either Mario or Luigi. The brother it comes down on must kick the egg back into the air. After several hits, the egg cracks and may dispense an item.
- Pocket Chomps - These items spawn a chain chomp that chases a brother. The player must hit that brother's button when he lands on an enemy. The more you do this, the faster the brother goes. When you miss, the brother slows down. When the chain chomp catches the brother, the turn ends. If a baby is present, it is possible to hit his button as he passes the enemy to do additional damage.
- Cannonballers - These items require all four brothers to be present. It launches them all into the air, and you must hit the corresponding button as he hits the enemy.
- Trampolines - These items work the same way, but the brothers can launch again if they hit at the right time.
- Copy Flowers - These items work the same way as the trampolines, but are faster and will hit the same enemy instead of random enemies.
- Mix Flowers - These items create an enormous fireball on the top screen. The brothers spread around the fireball, and one of them throws a fireball into the air. The player must mash this brother's button to build power in the fireball and keep it from falling. The fireball will periodically switch brothers, and if the wrong button is hit, iceballs are thrown at the fireball. This causes the fireball to descend. After the fireball falls, the turn ends.