I love all these fics, even the ones that aren't my own personal OTPs, and I heartily recommend them.
The father of X replaces him with a clone he finds a more “suitable” son. Only Y can immediately tell the difference.Identical (Lanning Cook, Smallville)
X builds a new life as a professor after Y is killed in action. Physics (and heartstrings) will never be the same again.Freedom's Just Another Word for Nothing Left To Lose (Synecdochic, Stargate: Atlantis)
Amnesia leads X to become the best and most effective criminal possible. Y is left a confused and frustrated police officer.Chicago’s Most Wanted (Speranza, Due South)
X is exiled to the seaside to recover from injury. A plaintive postcard summons Y to a forbidden tryst and true love.Wish I Wasn’t Here (M Fae Glasgow, The Professionals)
X, bleeding to death, sends a short text message telling Y how awesome he is. Y is less than amused (but saves the day).The Death and Resurrection of the English Language (Wordstrings, Sherlock)
X is “re-activated” leaving Y behind to be supported by his friends (and gently mocked as the “war widow”).When All of New York City Misses You (Leupagus & Sutlers, Hawaii 5-0)
Post alien invasion, X is held captive as chief scientist while Y leads the resistance. Smuggled notes lead to true love.When the Lights Go On Again (Seanchai & Elspeth Dixon, The Avengers)
X is 100% straight and 100% in love with Y. They both make their very best effort to make it work. Naturally it ends in tragedy, divorce and them still in love with each other.The Attempt (Yahtzee, X-Men: First Class)
X loves Y enough to forcibly resurrect him. Y misbehaves majorly, but it turns out he loves X enough to die (again) to resurrect him. Fortunately they have friends who work it out so that they both wind up alive.New Dawn Fades (Omphalos, Doctor Who)
X and Y drunkenly hook up and immediately regret it for the obvious reason. They wind up getting faux married in New Orleans.Road to Shambala (Astolat, Supernatural)
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