In the events of Sonic Adventure 2, it was deactivated and unable to fire until Eggman used it to blow up half of the moon. When he finally inplanted the last Chaos Emerald, the Eclipse Cannon was converted into a megabomb. If it detonated it would have been more massive than a supernova(according to Eggman in Sonic X). However, it wasn't.
It also hosts two Sonic Adventure 2 levels. The level Final Rush takes place down the cannon, with Sonic attempting to destroy it with his fake Chaos Emerald and Shadow trying to protect it. The level Cannon's Core also takes place at the core of the Eclipse Cannon. Both return in Sonic Generations.