The characters you play as in the multiplayer side of Mass Effect 3 won’t infringe on the single-player story.
“They will never be involved in the actual campaign of the main story,” producer Jess Houston said in an interview on the BioWare blog.
“It’s more like a side mission to the single-player. We don’t want to create situations where multiplayer players have something that single-player players couldn’t otherwise see.”
The multiplayer sections will have some narrative direction, though, which will be delivered through ambient means, such as commands issued via radio.
“At a high level, Shepard is marshalling the troops on behalf of the Earth Alliance so you are technically fighting for the Earth Alliance,” Houston said/
“From a story perspective, a lot of these groups have come together as a loose fighting force to stop the reapers therefore they don’t fly the same type of banners that would have existed in pre- reaper invasion days.”
Mass Effect 3 is expected on PC, PlayStation 3 and Xbox 360 in March 2012.