From the Super Mario Wiki, the Mario encyclopedia
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Pump Works is a location inside Bowser's body in Mario & Luigi: Bowser's Inside Story. This area appears to be in Bowser's esophagus. It is accessible to Mario and Luigi when Bowser drinks water from the Sea Pipe Statue in Plack Beach. Drinking water as Bowser floods the area, which allows Mario and Luigi to swim and certain objects to float. Once he stops drinking, the water will drain from the area. Mario and Luigi travel here to search for Princess Peach, but instead they find Toadsworth. This area also features ten Attack Pieces, that once gathered, allow Mario and Luigi to use the Fire Flower Special Attack. Also, it has an obstacle (a cannon that launches food for a giant Chombone) that is required to obtain the Stingler, an item that can be used to open the exit door resembling DNAs and access other areas of Bowser's body.
The area can be roughly divided into three parts. The first part starts from the entrance and consists of three chunks in a row. Mario and Luigi must clear the obstacles of this part to reach the orange pipe in the last chunk, which leads to the second part. The second part starts with a DNA-like door, which the bros. must first bypass and clear the rest of this part to find the Stingler, meeting Toadsworth and learning the Mini-Mario technique on the way. Once the bros. use Stingler on the DNA-like door, they can exit the area and unlock other areas of Bowser's body including Flame Pipe (their next area to check), Nerve Cluster, Airway, Chest Station, Nose Deck and Pipe Yard. Later in the game, after Mario and Luigi learn the Drill Bros. move in the Energy Hold, they can tunnel underground in the first chunk of the first area (the entrance) and go right to access the third part, where they can find ? Blocks containing items like Super Mushrooms, Star Candy, Guardian Socks and 1-Up Deluxes.
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