The Peps have two special abilities. They can merge with other enemies to make them stronger in speed, power, or defense, similar to the Ghoul Guys from Mario and Luigi: Partners in Time. They can also change themselves into a different type of Pep, similar to the Viruses from Mario & Luigi: Superstar Saga.
POW Peps are red with big muscular arms. POW Peps attack by getting close to Mario or Luigi and attempting to punch them, but Mario or Luigi can counter attack by using the Hammer at the correct time. If this enemy is fused with another enemy, the other enemy gets increased power.
DEF Peps are green with a shield next to them. DEF Peps do not attack at all, making it easy to defeat, despite the defense. If this enemy is fused with another, the other enemy will gain higher defense.
SPEED Peps are blue with shark like fins. These Peps attack by bolting towards Mario and Luigi which can give them the trip status effect. The brothers can counterattack by either jumping on them or staying still, depending on which area they are attacking. Unlike the other Peps this enemy doesn't fuse itself with another enemy to improve it's speed.
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