McKay/Sheppard thematic fic index >> Going to Earth
264 Hours by
Post The Siege III. McKay/male hooker -> McKay/Sheppard.
A Beautiful Lifetime Event by
Sequels/In Same Universe: Surprise,Double Bed
There's also Parenting in the Pegasus Galaxy by Brighid, but it's in a locked post. That's the story about Hyp getting her period.
A Little Bit Crazy by
Episodes: The Siege 3 & Intruder (the flashbacks part)
Set between The Siege 3 and Intruder
A Sheppard Family Story by
Sheppard/Other in the past, McKay/Sheppard in the present.
Ages and Ages Hence by
Crossover with Murphy Brown, where Joe Flanigan guest-starred. McKay/Sheppard, implied past Sheppard/Murphy.
Aliens Made Them Do It by url needed)
(Ascending Order by
Spoilers up to and including 3.20 "First Strike."
Close Enough by
Sheppard spends some down time with Rodney back on Earth after the siege. (On the wayback machine)
Conduct Unbecoming by
Rodney makes John take him to a class reunion and learns more than he expected.
Cool by
Crossover with Veronica Mars. Sheppard/McKay & Veronica/Logan.
Five Times Rodney McKay Didn't Call by
He hadn't expect to be homesick at college, not once he finally, finally, finally got there.
It Must Be Thursday by
Jack hates surprises. The Atlantis expedition has a few.
Just Tipsy, Awoken & Salutations by
Link to Salutations which has the links to Just Tipsy & Awoken.
Long Way Home by
Returning to Earth stirs up hidden yearnings and ghosts from Sheppard's past.
On a Clear Day by
John has always known that Rodney is braver than he gives himself credit for.
One, Plus Two, Plus Two, Plus One by
Set post-series as Atlantis gets prepared to go back to Pegasus, Keller resigns, Rodney follows her, and Rodney panics when he loses touch with John.
Rebirth of Legend by
Minor Caldwell/Weir, implied Ronon/Teyla & Lorne/Parrish.
Regions of Darkness and Light by
John and Rodney get sent to Earth to recover from a bad mission, while there Atlantis is partially declassified and someone has to do the press.
Something More by
Epilogue: Catch Your Breath. Rodney goes back to find John three years after John left Atlantis.
Square Peg by
An AU that branches off after the events in "Brain Storm"; set thirteen months later on Earth when Rodney has left the SGC and settled down with Jennifer. John arrives for a visit.
The Perils of Kissing John's Boyfriend by
John and Rodney go to Earth. Sam greets them.
The Raising Madison Series by
Becomes AU after "Trinity" but carries significant spoilers for "McKay and Mrs. Miller".
Things To Do In Denver When You're Dead by
Episode: The Intruder (the flashbbacks part)
Three Geeks Walk into a Bar by
Also implied Lorne/Parrish and Cadman/Zelenka.
Tonight by
Related story: A Cold Night for Crocodiles. Episode: The Return
Two men and a baby by
The natives give Rodney a gift: a baby clone of himself made with Ancient technology. Sequels: Second Watch, Fatherly Advice, Creation Myth
Unified Theory Series by
Everett was never drained by the Wraith and kept his position as military commander of Atlantis.
Wedding Day by
John and Rodney go back to Earth to get married... if the Wraith allows them to.