He is met first at chapter 4 of said game, where he is called ? and serves as the endboss. After beating him though, he takes Mario's identity and everybody belives he is Mario. The player then has to find out Doopliss' real name. Afterwards he is foughgt once again at the Creepy Steeple, this time accompanied by Mario's Partners.
After he is being fought off, he joins the Shadow Sirens as a replacement for Vivian. They all fight together against Mario at the shadow palace (Chapter 8) near the end of the game.