After the initial mission to Abydos, Murphy was left supervising the Stargate. They had sealed the gate so that no further intruders could come through without Earth's permission. However, when the remains of an Alien were found in the south pacific, severed in half, Murphy realized that this kind of mutilation was likely caused by failure to fully emerge from a Stargate.
He assisted Alexandria Klaus and the crew of the aircraft carrier Stormguard on a mission to deactivate the highly radiated Secondary Stargate on the Island of Doom. (Stargate: "Doomsday World 1", "Doomsday World 2", "Doomsday World 3", "One Nation Under Ra")