In CPU verse Mario and Luigi were natives of the CPU verse and were the first known batch of Humans to arrive in the new world of the Mushroom Kingdom another colonist that was sent there at a young age was Princess Peach, and she was raised by the Mushroom Kingdom as their princess
Mario then found a warp pipe that led to the direction of a Koopa Kingdom with a few differences like it had totems and Arcane marks and found a Koopa girl that looked like Princess Peach, since Mario had a kind heart, he asked her who she is and found out her name was Princess Koopa Peach that was when he realized that this is the princess peach of this universe. That was when someone else woke up Queen Bea, she was sealed by an unknown figure, and with Mario holding Koopa Peach's hand it broke the seal on Bea.
Even though Mario is not fond of Bowser (he was told that Bea was Bowser's wife and Koopa Peach is their first daughter) he is still willing to help those in need and he and his new friend help free Queen Bea they beat several creatures that were part of several evil groups from the CPU verse which awoken something in Mario making him one of Blanc's Generals under the command of the Lowe champion Klaue
After this Queen Bea was free and both Bea and Koopa Peach went back to Bowser and both were happy to see Bowser again (both had fun which might get Bowser Jr conceived), Bowser is not fond of Mario saving his wife and daughter since that means both are in debt to him (Koopa Peach doesn't mind as she fell in love with him and will make alliances with him). Bowser will still capture Princess Peach, much to Bea's annoyance as all three have their own way of concurring
