IGN just posted a story on a leaked 3 page plot outline for GoT. Originally it was supposed to be a Trilogy. While a lot of details in the outline are different than the actual story / show, the story is still about the same.
Quoting the text for reference;
Though Martin pitches the books as a trilogy (HA!) there are some bits that are unchanged in the published versions. For example, Ned Stark dies in almost the exact same manner, discovering the truth about Jon Arryn’s murder and then being sentenced to death by Joffrey. The biggest difference here is he manages to send Arya and Catelyn Stark out of King’s Landing beforehand.
This death then causes war to break out between the Starks and the Lannisters, though Robb was originally planned to fight Joffrey on the battlefield, with the spoiled young lion facing Robb without fear but ending up maimed. Sansa, meanwhile, would have married Joffrey and born him a son and heir. Eventually, she would have had to make a choice between her Stark family and her husband and would end up coming down on the side of the Lannisters, before coming to bitterly regret this later.
In more family disagreements, Tyrion would have removed Joffrey from the throne after being horrified by his actions. Jaime then proceeds to kill anyone with a great claim to the throne than him, including Tywin, before taking the crown himself and blaming all the crimes on Tyrion. The Imp is exiled and decides to ally himself with the Starks, which is where things get really interesting.
Having left King’s Landing before Ned’s death, Catelyn and Arya flee north, picking up Bran on the way and seeking refuge with the Night’s Watch, where Jon is. While here, Arya and Jon fall in love with each other but refuse to act on it because of the whole incest thing along with his Night’s Watch vow of celibacy. Interestingly, Martin says the situation changes once Jon’s true parentage is revealed, adding fuel to the fire of another popular fan theory about who they may be. Tyrion also falls in love with Arya, thus creating a love triangle in which Jon and Tyrion loathe each other. Arya doesn’t reciprocate The Imp’s feelings, however.
Unfortunately, the Night’s Watch aren’t really allowed to help their family out, so Cat, Arya and Bran are forced to flee further North beyond the Wall. They end up encountering Mance Rayder and Cat meets her death at the hands of one of the Others (the White Walkers from the TV show). Still, Jon manages to become commander of the Night’s Watch. So that’s nice.
The final plot point involves Daenerys, who not only invades Westeros a lot sooner, but does so after killing her husband Khal Drogo out of revenge for the death of her brother Viserys.
The final paragraph of the letter is blacked out, so we don’t know exactly how it was all supposed to or still could end. Having said that, Martin identifies five characters who would survive: Daenerys, Arya, Jon, Bran and Tyrion. Does this still hold true? We’ll have to wait and see.