The latest plot details reveal how this S.H.I.E.L.D. agent comes back from the dead, but be warned, there are heavy spoilers below, so read on at your own risk.
"In the pilot, it's revealed Nick Fury (Samuel L. Jackson), the ultimate super spy, faked Agent Coulson's death on purpose to motivate The Avengers. Some S.H.I.E.L.D. members were in on it (including, possibly, Maria Hill played by Cobie Smulders) but The Avengers were not. Their security clearance wasn't high enough. Coulson was forced to hold his breath as part of the ruse and that's a point of contention among his colleagues. After the fact, Fury moved him to a remote location until things died down, and then he was reinserted into duty at the time of the show."
The following details have not been confirmed by Marvel or ABC at this time. It should be pointed out that Coulson was killed by the spear of Loki (Tom Hiddleston) in Marvel's The Avengers. It seems highly unlikely that the villainous Loki would be in on this ruse, so how exactly could they "fake" Agent Coulson's death? We'll have to wait and see if ABC picks up Marvel's Agents of S.H.I.E.L.D. to find out.