Crypto Energy (CE) is the unit for experience points in MCH.
My defeating Enemies in Quests you collect CE. (Keep in mind if you are defeated during a quest you aren't awarded any CE)
Heroes and Extensions can utilize CE to Level Up! Also, CE for Heroes can be purchased via GUM.
The CE for Extensions is level up depending on "Absorb" Also the CE within an Extension can be "Absorbed" into that of another Extension.
As for other uses, putting CE to your CE Barrel lets it be used to participate in other Content within MCH.