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I like to think that Bowser's wife was a kind and beautiful woman who Bowser instantly fell in love with.
They got married and had Wendy first, yet they were thinking about having other kids as well
Unfortunately, she also had a fatal disease and never told Bowser about it because she wanted to live out the rest of her days in happiness.
After giving birth to Jr. A couple of days later, she sadly passes away. Bowser becomes utterly heartbroken and vows to never love another again.
Bowser doesn't tell Jr. the truth about his real mom cause he doesn't want to think that her death was his fault because when she was pregnant with him, that weakened her immune system
Maybe Bowser can someday find love again, and if it isn't with Peach, then maybe it's with a certain green plumber