According to Valve's press release:
Mann vs. Machine is a new co-operative game for Team Fortress 2 that lets you and five friends wage a desperate battle to stop a lethal horde of robots from deploying a bomb in one of Mann Co.’s many strongholds. Take advantage of breaks between waves to upgrade your abilities and weapons. Survive all the waves in any of a variety of missions to earn incredible loot.
The folks over at The Escapist have an easy to digest break-down of the 5000 piece ARG campaign detailing the storyline behind the new mode.