I've attempted to list the stories in the main timeline in the order they take place. For the most part this works, but with my vignette series Imagine What You'll Know Tomorrow, it does get a little complicated, since I posted those in the order the prompts were available and not in the order they take place. Some vignettes take place after some of the other stories.
Man of Mystery Ecks and Wye and Count Zark, on a foggy Halloween night. Pure cracky nonsense.
Imagine What You'll Know Tomorrow A series of vignettes written for a month-long challenge on the Livejournal community 31_Days. Pieces are listed in the order they were posted, but not in the order they take place. One storyline tells of Ecks and Wye's days in the organization and of some of the conversations they had while growing closer. Another storyline follows them in The Odd Man Affair and details their survival. A third tells of their escape from England and starting over fresh in New York.
The Hyde Park Affair Only available in The Kuryakin File fanzine. Illya and Napoleon discuss what happened in The Odd Man Affair and whether Illya's stabbing of Mr. Ecks was brutally unwarranted.
The Mist of Yesterday Immediately after returning to New York following The Odd Man Affair, Illya is visited by what seems to be the ghost of Mr. Ecks. He is a restless spirit, to be sure.
The Shards of Our Past Affair Despite Illya dismissing Mr. Ecks at the end of The Mist of Yesterday, Ecks cannot be at peace. He continues to haunt Illya, for a reason neither of them understand.
Where We Burned the Bridge Following the destruction of the organization, Mr. Waverly and Mr. Wye accidentally meet at Mr. Zed's house.
The Haunted Mansion Affair Napoleon and Illya investigate weird sounds in an old mansion while they are unknowingly stalked by Ecks.
The Return From the Dead Affair Illya learns the identity of his stalker.
A Journey Among the Dead A creepy oneshot in which Ecks and Wye chase a thief through Bayside Cemetery in New York.
The Cat on the Flagpole Affair Napoleon and Illya try to rescue Mrs. Pumpkin-Klanger's Siamese cat from a horizontal flagpole and are joined by Mr. Ecks.
The Peaceful Meadows Affair Napoleon and Illya go undercover to investigate a gated community where residents disappear after committing the slightest infractions. They discover Ecks and Wye are undercover there for the same reason. This story reveals Ecks and Wye's real names, albeit they never actually say the names are theirs and not just aliases.
The Fifty-Millionth Frenchman Affair (Currently unfinished.) The follow-up to The Peaceful Meadows Affair. Mr. Waverly has sent Napoleon and Illya to Los Angeles to find a rogue extremist, Ms. Cue. He pays Ecks and Wye to go with them. The case ends up a complicated, twisted mess, as Illya discovers he has a double living in the city and as enemies try to get hold of Ms. Cue first. In a subplot, Illya and Ecks are each remembering the encounters they had when Ecks left his body, but neither wants to ask the other about it.
Clash of the Spies Ecks and Wye tangling with Siegfried and Shtarker of KAOS. I got plunnied for this while watching Get Smart and thinking that Ecks and Wye probably often got into the kinds of problems Napoleon and Illya often do in the episodes. I also came up with the idea that the various extremist organizations probably clashed with each other. KAOS is canonically described as a terrorist organization, and THRUSH certainly does many similar things to what KAOS does. So they are probably both similar and just as bad or worse as the unnamed organization for which Ecks and Wye worked. And perhaps none of them wanted the other groups to get ahead instead of them, heh.
You Don't Have to Lay Your Life Down Based on a dream, but turned into a Robert Vaughn/Napoleon Solo tribute after Robert Vaughn's sad death on November 11th, 2016. Napoleon ends up pinned down by THRUSH in an alley with Mr. Ecks.
Other Timelines
How Do You Like Them Apples? A vignette series involving the character Pinto from The Fugitive episode Masquerade and how he interacts with Napoleon and Illya. This does include my earliest attempt at reviving Ecks, but I didn't remember the episode very well at the time and there is no mention of Wye. I do not consider this version of the events part of my canon, but I took the plot of Ecks stalking Illya and reworked it later. I also still consider Pinto's involvement in U.N.C.L.E. to be part of my canon. Under his real name, Lucius Bowen, he briefly appears in The Peaceful Meadows Affair and sometimes is referenced in other stories.
The Aftermath of The Fortune Cookie Affair I participated in a Round Robin and had Ecks and Wye around as minor players. After it wrapped up, I was plunnied to write this to wrap up their involvement. The Round Robin is another timeline since it has a different version of how Napoleon and Illya found that Ecks and Wye were alive. I'll try to get a link to the Round Robin itself if I can find a place where all the pieces are gathered together. My favorite part? When Alynwa wrote a segment where Wye flips on Angelique when she hurts and perhaps poisons Ecks.
Other Stories
The following stories have no real relation to the Ecks and Wye stories, but they are other U.N.C.L.E. stories I've written.
The Night of the Deadly Codename A huge crossover story, mainly with The Wild Wild West, Cannon, and The Fugitive in addition to U.N.C.L.E. Mr. Waverly is the main U.N.C.L.E. character aside from Lucius, who joins U.N.C.L.E. at the beginning of the story. Napoleon and Illya come along later and are prominent in the last several chapters.
The There is Nothing Wrong With Your Television Set Affair Sometime after The Prince of Darkness Affair, Napoleon and Illya attend the engagement party for Annie Justin and her fiance. Some of the guests give Napoleon a turn.
Faded Into Gray Illya has gone missing on a mission ... and his spirit seems to have appeared to Napoleon to tell him Goodbye. This was inspired largely by the song I Guess It Doesn't Matter Anymore by Blackmore's Night.