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I get that the dark-haired seed is strong and we can infer that the three Baratheon-Lannister children are not Robert's. But how did Eddard correctly guess that the real father was Jaime, and not some other random guy that Cersei was with?

Bran could have been pushed by the window with that knowledge also. Isn't it also possible that the golden-haired seed is stronger in comparison to another gene, due to which the children were blond?

Finally, the Queen's brother is the last person anyone would expect her to have an affair with. So what did I miss that points the finger at Jaime Lannister?

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“the Queen's brother is the last person anyone would expect her to have an affair with” — as Cersei and Jamie discuss (at least in the TV show), royal Targaryen siblings had children together, so I don’t think it would be thought of as inconceivable. – Paul D. Waite Aug 21 '14 at 13:37
@PaulD.Waite I wish Joffrey had been inconceivable. – Moogle Aug 21 '14 at 13:42
You pose an excellent question. As I recall, Cersei readily admits that the children are Jaime's, but why would Ned guess that? – TLP Aug 21 '14 at 14:49
Related:… – Mooz Aug 22 '14 at 2:04
Jaime and Cersei were also caught together when younger by a servant at Casterly Rock. Their mother moved their bedchambers to separate ends of the castle. It's not clear to what extent this was known by anyone outside of the Lannister family, though. – Rob Sobers Aug 31 '14 at 0:27
up vote 35 down vote accepted

After the assassination attempt, it seemed obvious that Bran was pushed because he knew/saw something that he shouldn't have. Once it was clear that Cersei was cheating on Robert and bearing another man's children, it'd be a pretty good guess that Bran caught them in the act.

So from there, Eddard would only need to consider every member of King Robert's retinue who visited Winterfell. All of the adult noble men left Winterfell with the king and Eddard to go hunting during the hours that Bran was pushed... except for Jaime, who stayed behind to protect the queen. Jaime, who had previously shown himself capable of dishonorable violence. Jaime, his sister's stalwart defender. Jaime, who would have been in close proximity with the queen during the time of all three conceptions.

Couple that with how overwhelmingly all three Baratheon children had the Lannister look, and I don't think it's that hard of a conclusion to draw.

Also keep in mind, Eddard summons Cersei to the garden because he has discovered "the truth that Jon Arryn died for." Cersei is the one who starts talking about how Jaime would have killed Robert if he knew he hit her. It's that comment that leads Eddard to say, "Your brother... or your lover?" So it may be that Eddard summoned Cersei knowing that the kids weren't Robert's, but only suspecting that Jaime was the father. Cersei assumed Eddard knew everything, and basically telegraphed that they were lovers.

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The last paragraph is a good description: Eddard guesses, and Cersei admits. It is still quite the stretch to guess. Jaime is the type who protects his family, as we have seen he attacked Ned when Catelyn kidnapped Tyrion. – TLP Aug 21 '14 at 14:52
Also, the all of the other children that Robert had fathered had dark hair. Which Jon Arryn had helped to send away so they were not discovered. – Craig T Aug 22 '14 at 1:18

When Sansa has her outburst in AGOT Chapter 44, she says:

I'll give him a son with golden hair...

Hair color finally makes Ned realize the truth, that Robert is not the father. One of the the next logical questions is who could be the real father. Ned knows that Jaime and Cersei are close, and according to this description of Jamie's appearance:

Jaime has the quintessential Lannister look, with bright green eyes and golden hair.

And his son:

has the Lannister look and is tall for a boy his age, with blond curly hair. Known to be handsome, he has bright green eyes, pouty lips and an evil sneer.

Who else lived in close proximity to the Queen in King's Landing for many years and was tall with golden hair and green eyes? Once Ned came to his first conclusion is not much of a stretch for him to reach this one as well.

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Also he goes through that book and notes that the Baratheons all have black hair, I believe. – Mark Rogers Aug 21 '14 at 14:20
Not to mention Jon Aryyn's message "The seed is strong." – MyCodeSucks Aug 21 '14 at 15:22
Well if Lannister hair & eye color are dominant traits, then the Queen's lover could have dark hair & eyes and the offspring would still be blond-haired and green-eyed. – RobertF Aug 22 '14 at 21:18
@MyCodeSucks MarkRogers You are missing the point. The discovery path is A: Robert is not the father, because then the hair would be black. B: Jaime is the father because....? – TLP Aug 29 '14 at 12:18

The book that both Jon Arryn and Ned Stark were killed for looking at proved that Robert Baratheon's children by Cersei are not his biological children.

That book was a genealogy of all the great houses that showed what traits from each house bleed true in the children, regardless of the parentage. All Robert's children, not from Cersei were dark colored just like him. And many of them looked like him.

All Jon Arryn and Ned Stark had to do was take one look at Robert Baratheon's children by Cersei, and know that none of them were his.

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While true, this doesn't explain how Ned figured out it was Jaime. – Null May 6 '15 at 20:31

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