Armageddon Missiles are part of a game mechanic which is designed to break up stalemates. They are acquired automatically at Techlevel 20, and will fire every level thereafter from all Tech Labs under your control, dealing 1500 points directly to a base's structure, ignoring armor. If your team does not control a techlab, the missile has nowhere to emerge from.
The damage can be upgraded to 3000 with the Experimental Armaggedon Missile upgrade.
In the late game phase, controlling the techlabs is usually vital to winning.