As commander of Atlantis, Woolsey had his fingers in all of the city's operations, micromanaging every aspect of the operation as he could. If it were not for his, as some would call it, 'vigilance' the misdirection of a few key supplies to offworld allies would have gone totally unnoticed.
Woolsey eventually tracked the 'snafu' back to its source...Colonel Sheppard. Woolsey fully investigated the matter, then had Sheppard arrested and sent back to Earth for a hearing and subsequent trial, but not before the two exchanged harsh words on the precipice of the stargate's event horizon.
Removal from DutyEdit
Sheppard eventually returned to Atlantis along with Stevenson and subsequently took over the city. Woolsey and all base personnel still loyal to Earth were sent back through the stargate, leaving Sheppard and company in charge of the city of the Ancients. Woolsey was literally 'kicked' back through the gate by Sheppard, where he had the unfotunate task of relating to his I.O.A. superiors and General Landry the unexpected turn of events.
Woolsey volunteered to accompany General Carter on her mission to retake Atlantis, traveling with her aboard the Odyssey for more than a year before the mission came to an unfortunate end, seeing the crew of all three 304's captured and held inside Atlantis where they were offered the choice to stay and aid the rebels or return back to Earth through the stargate...without their ships.
Woolsey chose to return to Earth, of course, but before he was sent through the gate he thought something pithy towards Stevenson and inadvertantly opened up his mind to some critical information that caught the Alterra's attention. Woolsey was grabbed in a telekinetic hold and raised off the floor while Stevenson dug deep into the memories Woolsey was inadvertantly shining a light on.
When the memories of the I.O.A.'s plans to capture and kill Stevenson, at Woolsey's suggestion, made their way to the surface Stevenson saw the man for the tie-wearing camouflaged villain that he was and snapped his neck. The Alterra tossed Woolsey's body back to Earth through the stargate, along with a set of Woolsey's memories in the mind of General Carter so the SGC and others would know the particulars of what had happened.
Woolsey's death and subsequent, unceremonious return of his body through the stargate delivered a stark, unexpected message from the Alterra. Up until this time the Tau'ri had always viewed the Ancients as timid, peaceful, almost pacifistic souls who would prefer discourse over violence. It was such a type of person that the bureaucracy of the I.O.A. manipulated on a daily basis, hiding behind a facade of civility and physical weakness up until they had total control of the situation. Only then would they reveal their true, dark colors.
Woolsey's death made it shockingly clear that the Ancients were not only smart enough to see through the ruse, but that they were not pacifistic negotiators. Instead they were quick thinking, quick to act superhumans that would respond with an appropriate measure of force to misdeeds.
Succinctly, the message sent to Earth was: DON'T MESS WITH THE ANCIENTS