If you were confused with what was shown in the recent Mass Effect 2 trailer, OXM brings us a small blurb straight from BioWare that hints as to what exactly is going on.
"If Shephard is after Cerberus, why is a Geth shown?" Bioware asks OXM. "Unless the teaser implies the Geth are working for Cerberus... but it's a pro-human organisation, so why would they employ the Geth, an alien-created machine race? All this would only make sense if Cerberus was under the control of the Reapers..."Sounds reasonable.