A mission goes terribly wrong for SGA-1. McKay messes up something greatly (can be anything, but has to be a big mistake), which causes Sheppard to be captured. The resting SGA-1 members must return to Atlantis alone.
Back in Atlantis (choose whatever season you want to have whomever you like best in charge) there is a decision made to send McKay home because of his mistake.
McKay then runs away right into danger's hands to save Sheppard and redeem himself. Must have Sheppard/McKay pairing, NC-17 preferred but not necessary, happy ending.