From the Super Mario Wiki, the Mario encyclopedia
Lightning is a captain command in the Minion Quest: The Search for Bowser mode of Mario & Luigi: Superstar Saga + Bowser's Minions and the Bowser Jr.'s Journey mode of Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey where only Iggy can use it. When used, the captain will send cascading lightning bolts on all members on the opposing squad, shrinking them, similar to Lightning in the Mario Kart series. The effect varies for all squad members.
In Bowser Jr.'s Journey, this captain command is featured prominently in the level Be Leery of Lightning, where at the start of every round the enemy captain will use this command, and all allies will remain small for the entire round. However, enemies summoned via Larry's Call for Backup command or clones from Wendy's Doppelganger move will still be unaffected.