Apparently there was a gap between when the pilot was made and the show was picked up. In the interim, it looks like Greg Germann did another pilot called "In Case of Emergency," which got picked up for fall on ABC.

Ed Quinn's character, Nathan Stark, seems to be the replacement character. There's a few other changes from the pilot, like Section 5 now seems to be all about the mysterious artifact instead of where the high-tech military stuff was developed.