Wolverine was captured at some point and was hooked up to a machine and acted as a central nervous system for the Sentinels, giving them his appearance as well as his honed hunting and tracking skills. This aided Susan Storm's cause as the Sentinels were able to arrest many super powered beings and mutants alike.
Logan presumably spent many years acting as the Master Mold for the Sentinels until he was one day visited by heroes from the past, including himself. The Wolverine of the past noted that his future self seemed to look even younger than he, even though it was 20 years in the future. Master Mold managed to whisper something to Logan, at which point he used his claws to slice right through Master Mold's spine, severing the link to the Sentinels, and, presumably, killing him.