Energon and Cybertron occur in different time dimensions. No matter where you are, good and evil must balance out. In Energon, Unicron (the ultimate evil) is destroyed.

This created a gigantic shift in the balance, which created a "grand black hole" which tore though time and space. It will destroy the past, present, and future if it isn't removed somehow.

Cybertron episode 1 picks up when the Transformers evacuate Cybertron. Without a clue on how to battle the black hole, they hear about 4 "planet cyber" keys that will unleash the ultimate power to fight it. Nobody knows wtf the ultimate power is, but that's their only shot.