1) The Tarot Series by LJGray (Abandoned WIP – 151, 901 words/21 chapters): http://qaf-fic.com/atp/viewstory.php?sid=1167 [Season 3 AU: JT Left BK For Ethan/JT & Ethan Fizzled Out/JT Goes to Europe For Summer & Decides to Stay in France Permanently & Not Return to Pitts/BK Finds Out JT Blackmailed Kip/BK Finds Out JT’s in Europe From Ethan/BK Goes to France to Work With Client – Gilles Michaud/BJ Run Into Each Other in France/BJ Decide to Pretend They Don’t Know Each Other & Form New Friendship/BJ Discuss Relationship/JT Tells BK He Remembers Prom/BJ Start Fucking/BK Romantic/JT Decides to Leave With BK]
Note: It seems there are only 2 chapters missing from this story (one that was written and lost and the final chapter that was supposedly never written). Even though this story seems to be abandoned I would still recommend reading it. It ends in a relatively good place (as long as you ignore a warning Mysterious Marilyn gives prior to the final chapter posted) and it’s so long and so good it’s definitely worth a read.
2) Parameters by Scheming Star (23,597 words/15 parts): http://schemingstar.livejournal.com/?skip=14&tag=fic%3A%20parameters [Post-Season 5: JT in NY/JT Has Brain Tumor & Is Referred to Specialist in Pitts/JT Tells Gang About Brain Surgery/BK Helps JT/JT Goes Through Chemo/BJ Reunion]
3) Changes by Edom (17,558 words/14 chapters): http://archiveofourown.org/works/133003?view_full_work=true [Post-Season 2: JT Goes to LA For Internship/He Returns to Pitts With Dark Hair & Muscular Body/Everyone Thinks JT Trying to Look Like BK’s Usual Tricks/JT Tells BK He Changed His Look to Stand Out in LA/BJ Discuss Relationship/BJ Call Each Other Partners/BJ Go to NY For BK’s Birthday/Jealous Michael/JT Yells at Deb & How She Treats BK]
4) A Light Shining Through The Darkness by Bigdogz09 (44,206 words/10 chapters): http://www.midnightwhispers.ca/viewstory.php?sid=1646 [Circa Season 3: JT Left Babylon With Ethan/Now JT is Missing/Horvath Questions BK/Horvath Questions Chris Hobbes & Realizes CH Has Feelings For JT/Towel With JT’s Blood Found/BK Punches a Window & Injures Himself/Ethan Stabbed & Tried to Kill JT When JT Told Him He Was Going Back to BK/JT in Hospital With Many Wounds/Jealous Michael/JT Stays Away From BK Because He Thinks He’s Now Damaged & Ugly Due to His Scars/JT Stalked By Reporters & Anti-Gay Whackos/JT Moves to Artist Colony in Michigan/The Gang Has No Idea Where JT Is Except For BK/BK Visits JT For His Birthday/BK Has New Tattoo He Shows JT]
5) Crossing the Line by Bec2224 (40,043 words/4 chapters): http://archiveofourown.org/works/932369?view_full_work=true [Post Season 5 -- 8 months later: JT in NY/Anti-Michael & Anti-Mel/Michael Doesn’t Understand BJ Are Still Together Even Though JT’s in NY/BK Finds Out Michael Has Been Sneaking Into His Loft & Fucking a Hustler That Looks Like BK/Lindsay Left Canada & Returned to Pitts After Mel Threw Her Out/Lindsay Tries to Convince BK To Marry Her/BK Ends Up Sending Lindsay to Psychiatrist for Two Weeks/Ben Leaves Michael/JT Returns to Pitts For Good]