Another day, another A Song of Ice and Fire alternate-universe fan-fic from the Internet forum for you. This one is entitled "The Falcon Has Flown." It diverges from canon on the smallest of matters--Jon Arryn, the Hand of the King to the neglectful Robert Baratheon, agrees to see one more petitioner. It turns out it's the ambitious, loquacious Justin Massey. He's intent on getting some lands and keeps talking for an hour, delaying Jon going to lunch. This delays Jon getting poisoned by around a day or so, allowing him to send his sickly son Robert Arryn to Dragonstone to be fostered by Stannis Baratheon.
At this point he's aware that Robert's children aren't actually his, but he doesn't intend to tell Robert until after his son is safe on Dragonstone with Stannis, who also knows what's going on. Once "Sweetrobin" is safe, he thinks a confrontation with the Lannisters is coming and is counting on his protegee Petyr "Littlefinger" Baelish to keep the Gold Cloaks on the right side.
Well, we all know how trustworthy Littlefinger is when there's the possibility of the rigid, hands-on Stannis becoming king. From the end-note in the first chapter, it's clear Jon Arryn is going to die before he can share his suspicions with Robert. I'm guessing that the events of A Game of Throneswill generally follow their canonical course rather than Robert flipping his lid, going after Jaime and Cersei with his warhammer, and starting a war with his evil-mastermind father-in-law Tywin Lannister.
However, once the War of the Five Kings begins, Stannis has an advantage he didn't have in canon--the sole Arryn heir as a hostage. In canon Yohn Royce led a group of nobles who wanted to intervene on the side of Robb Stark against the Lannisters, but Jon's wife Lysa managed to maintain the neutrality of the Vale, ostensibly to protect her son. With her son as a hostage and much of the Vale nobility wanting war with the Lannisters, Stannis might find himself with a very reluctant and difficult (but given his situation, welcome) ally. And then there's Littlefinger, Lysa's lover, who most assuredly does not want Stannis to become king. Treacherous doings are afoot...
The author says he updates slowly, but my experience with fanfiction.net and my own writing groups, having a lot of readers is a strong incentive to update more regularly. Prove my theory right by following and reviewing!