What, you mean they died? Then how did they appear in Hotel Mario and Yoshi's Safari?
Let me give you a real world example:
This guy goes to the store for some coffee.
(SMB)
He gets the coffee, then leaves.
(Bowser defeated in SMB)
When his children are of age, he takes them along as well.
(SMB3, SMW, HM, YS)
They grow up, and leave the house. The man goes for coffee by himself.
(SMRPG, SM64, PM)
He has another child, and when he is of age, he takes him for coffee.
(MP's, SMS)
The End.
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A shiny! It came out of the yucky!