Paper Mario: The Thousand-Year Door
In Paper Mario: The Thousand-Year Door, it was revealed that the X-Nauts kidnapped Princess Peach under Sir Grodus' orders. Afterwards, they were sent back to Rogueport to find the map that she had. However, they were unsuccessful and their commander, Lord Crump, notices Goombella and were ordered to capture her. However, Mario came onto the scene and managed to defeat him. Back at the Fortress, one X-Naut found out that Mario took the Crystal Star and Peach accidentally revealed his name to Sir Grodus. Grodus, now aware, sends the X-Nauts to The Great Tree to find the Crystal Star there. At The Great Tree, the X-Nauts quickly took over replacing the doors with locked up ones and even locking up the Punis to find the Crystal Star. As soon Mario enters The Great Tree, two X-Nauts attack him. Mario defeats him and heads further into the tree. Another X-Naut gets knocked out my Ms. Mowz and two others attempt to stop Mario from reaching Lord Crump when the tree was about to get destroyed. After Lord Crump was defeated yet again, the X-Nauts were forced to leave and had to contact Sir Grodus about it. The X-Nauts weren't mainly seen again until Chapter 5 where one confirms that "Four-Eyes" is actually Lord Crump. After Mario gets the Crystal Star from Cortez, Lord Crump and the X-Nauts launch an attack demanding Mario to hand over the Crystal Star. The X-Nauts were used as a flag and battled against Cortez's crew. The X-Nauts also aided in the fight against Mario alongside Lord Crump and they were all defeated by Mario's group. The X-Nauts are seen again at their Fortress as roaming enemies. It was revealed by Lord Crump and TEC that Grodus has already left for the Thousand-Year Door with Peach. After Mario finally defeats the Shadow Queen, the X-Nauts have stopped appearing due to their leader being nothing more of a head now.
Super Paper Mario
In Super Paper Mario, the X-Nauts do not make an actual appearance but Francis, the boss of The Bitlands and a mega fanboy watches a science fiction television series about the X-Nauts called "Starship X-Naut", and he also collects X-Naut action figures, indicating that the X-Nauts did indeed keep their promise and not cause anymore mischief.
- When the X-Nauts were running away from The Great Tree after Lord Crump was defeated, one of X-Nauts tripped as he was running away. This alludes back to the running gag of the Shy Guy that keeps tripping back in Paper Mario.