That sounds about right. The matrix place the guy was at noticed he was missing after he uploaded into a human body that was grown for him, so they restored him from backup. This version is like the version that first showed up, so he still was into his fiance, so they become a couple again. "Original" guy is in the real world with the woman he fell in love with and they try to do stuff IRL to stop the plot related to the open-source free upload world that will just kill people. At the end of season 3, the real world version of the guy gets captured and is allegedly killed.
Based on the trailer, it sounds like maybe he did die, but was uploaded to the general internet or something?