From the Super Mario Wiki
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Command Blocks are blocks in the Mario & Luigi series. They appear during battles, so Mario, Luigi, Baby Mario, Baby Luigi, and Paper Mario can jump under or Bowser can punch under the block that they want to choose. The block they choose determines the move they want to do.
In Mario & Luigi: Paper Jam, when Mario, Luigi, and Paper Mario are locked away in Twinsy Tropics Dungeon, a team of Hammer Bros confiscate the trio's command blocks to hinder their fighting capabilities. The three must defeat the Hammer Bros using a combination of First Strikes and counter attacks in order to regain the command blocks.
In volume 35 of the Super Mario-Kun adapted from Mario & Luigi: Partners in Time, Luigi and Baby Luigi hit the Flee command block to run away from a Snoozorb, much to Mario's irritation, and therefore breaking the fourth wall.
Mario & Luigi: Bowser's Inside Story / Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey
* - Replaces Special Attacks and SP for Bowser in the remake.
Mario & Luigi: Superstar Saga
Mario & Luigi: Partners in Time
Mario & Luigi: Bowser's Inside Story
Mario & Luigi: Dream Team
Mario & Luigi: Paper Jam
Mario & Luigi: Superstar Saga + Bowser's Minions