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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)
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)