I must realized I don't think they've ever explained what chemical x was…

This is now my headcanon.

These are my thoughts:

Samurai Jack takes place in the alternate timeline where Aku wasn't defeated

Powerpuff Girls takes place after Jack makes it back, defeats Aku, and lives happily ever after
Utonium is a descendant of Jack
Chemical X consists of the physical remains of Aku
All the monsters in Townsville are manifestations of the remains of Aku's influence

I loved thinking this and making these connections when I was a kid. Although, that ironically means that the girls are using Aku's power against himself.