An AU request? Really?
Premise: AU ending to "Time After Time." Dean and Eliot were successful in killing Chronos, thereby trapping Dean in 1944. Dean becomes Eliot's partner in the past (with appropriate adventures ensuing), while Jody becomes something of a partner to Sam in the present.
Interesting thing: When Jody and Sam are going through Bobby's books, they find an old hunting journal, dating from 1944 through . . . up to the author. It's tucked away in a seldom-used box (it was in the storage locker, after all).
It's the journal of DW. Scattered throughout are notes to Sam, some hunting related, some personal. A casual reader might wonder if DW had the quirk of naming his journal "Sam," or who this mysterious "Sam" might be. Sam and Jody know better.
If the author could find a way to return Dean to the present after not too much time has passed, that would be delightful. If not, a total AU wherein Dean never makes it back would be heartbreaking and induce a desire for chocolate.