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In the first book/series of ASOIAF/GOT, Ned Stark discovers that

Cersei's children are not King Robert's, but Jamie's.

He discovers it by retracing Jon Arryn's steps in discovering the secret. He finds out most of this information through Pycelle, who told Ned the final movements of Jon Arryn and even provided him with part of the proof via the book of genealogy of the Baratheons through the ages.

It is found later on in the story that

Pycelle is a Lannister spy and would want to keep the secret of the royal children's true lineage hidden.

I was under the impression that Pycelle knew what Jon Arryn had discovered before he died, particularly because Jon kept muttering "The seed is strong".

Clearly then Pycelle understood that Ned was about to discover the same truth. So why didn't he lie about what Jon was doing?

I understand that he wants to keep his true allegiance a secret, but he could have just been less helpful to Ned or feigned ignorance about what Jon was doing before he died.

Did he think Ned wasn't clever enough to figure out the truth as well? Or did he want to help him to ensure that he was kept in the loop, and would know everything that Ned had discovered?

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    It may be hinted, but maybe it is not what really happened ? Where are you in your reading of the books ? – Kalissar Mar 30 '15 at 11:06
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As soon as Ned walked into Pycelle's chambers and began asking about Jon Arryn's final days and the manner of his death, it was painfully obvious that someone had been feeding Ned information. Jon Arryn was old, and Ned had no reason to doubt the official cause of death... unless someone like Littlefinger or Varys said otherwise.

Pycelle had no choice but to feed accurate information to Ned. If he lied in some way that Ned's sister-in-law could contradict, he would have outed himself as a conspirator. The only publicly known information about Jon Arryn's last days is that:

a) he poured over a book from Pycelle

b) he visited a bunch of unspecified locations, so that's all Pycelle told him.

And it's worth noting that the only information Pycelle gives Ned that's of any use is basically useless on its own. Ned could have read the genealogies and lineage of the houses of Westeros for his entire Handship. But it wasn't until Varys clued Ned into the fact that Stannis had been investigating Robert's bastards that he was able to put two and two together.

13

We know from A Clash of Kings that Pycelle knew about Jon knowing that dangerous secret:

[Tyrion] "And what was Lord Arryn plotting?"
"He knew," Pycelle said. "About... about..."
"I know what he knew about," snapped Tyrion, who was not anxious for Shagga and Timett to know as well.
"He was sending his wife back to the Eyrie, and his son to be fostered on Dragonstone [Stannis' castle, my comment]... he meant to act..."
"So you poisoned him first."
"No." Pycelle struggled feebly. Shagga growled and grabbed his head. The clansman's hand was so big he could have crushed the maester's skull like an eggshell had he squeezed.
Tyrion tsked at him. "I saw the tears of Lys among your potions. And you sent away Lord Arryn's own maester and tended him yourself, so you could make sure that he died."
"A falsehood!"
"Shave him closer," Tyrion suggested. "The throat again."
The axe swept back down...[...] "I tried to save Lord Arryn, I vow-"
[interrogation..]
"Yes," he whimpered, "yes, Colemon was purging, so I sent him away. The queen needed Lord Arryn dead, she did not say so, could not, Varys was listening, always listening, but when I looked at her I knew it. It was not me who gave him the poison, though, I swear it."

So obviously at the point where Ned Stark asks about Jon Arryn's dealings, Pycelle knew not only who had killed Jon Arryn (or so he thought anyway), but why. So it would stand to reason that he would try to mislead Ned Stark if he could. There is no explanation in the books, but at a guess, it would either be because he did not realize the importance of the information (not likely), or he did not dare withhold information, which Ned might find elsewhere, for example from Varys. Or it could just be that GRRM did not consider that angle.

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    I guess it's even possible that Pycelle thought Ned finding out would lead to his (Ned's) death, and that suited him just fine. Risky, but possible. – Geobits Mar 30 '15 at 15:19
  • With Robert still alive, that would be very dangerous. And that would be doing the opposite of what he did earlier, when not trying to save Jon. – TLP Mar 30 '15 at 15:22
  • I'm not saying Pycelle would kill him, just that he didn't like Ned much and wouldn't mind if he got killed for sticking his nose in it. Robert could be mad about a dead Ned, but if Pycelle's only hand in it was to help him as Ned instructed, it's hard to blame him. – Geobits Mar 30 '15 at 15:29
  • No one said Pycelle would kill Ned, I understood what you meant. What I mean is that if Pycelle helped Ned discover that Robert's children were all Jaime's, Robert would kill Cersei. Which is what Pycelle tried to prevent in the first place. – TLP Mar 30 '15 at 15:31
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    Yes, but in the meantime, he should help Ned for appearances, which was my point. Help him along to his (very likely) death while appearing to be on his side, so Ned wouldn't grow suspicious of him. If Cersei lost out in the end, he would have been a key in making that happen (from Ned and Robert's POV). Playing both sides doesn't seem out of character. – Geobits Mar 30 '15 at 15:40
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It is true that Pycelle is a Lannister loyalist. When aked about this, author George R. R. Martin said:

[Why is Pycelle so loyal to the Lannisters?]

There´s backstory yet to be revealed, certainly, but if you asked Pycelle he would insist that he was acting in the best interests of the realm.
-http://www.westeros.org/Citadel/SSM/Entry/Asshai.com_Forum_Chat

However, throwing Ned off the scent in this instance would have come back to bite him.

Sneaky little Pycelleses
You see, Pycelle always tries to appear as though he is serving the realm, and not just one single House or his own private cause. For that reason, he didn't want to make it suspicious that he was throwing Ned off the scent. Ned was not stupid (he was clouded by his honour, but not stupid) and he would have found out one way or another, at which point it would have been obvious that Pycelle was deterring his investigation.

Calculated risk
Pycelle also took the calculated risk that showing Ned the "book", may have had a chance that Ned wouldn't put two and two together, making the book as pointless as Ned initially thought.

Out of the mouths of babes
It was after all something that Sansa and Arya said that made Ned click:

“He is!” Sansa insisted. “I don’t want someone brave and gentle, I want him. We’ll be ever so happy, just like in the songs, you’ll see. I’ll give him a son with golden hair, and one day he’ll be the king of all the realm, the greatest king that ever was, as brave as the wolf and as proud as the lion.”
Arya made a face. “Not if Joffrey’s his father,” she said. “He’s a liar and a craven and anyhow he’s a stag, not a lion.”
Sansa felt tears in her eyes. “He is not! He’s not the least bit like that old drunken king,” she screamed at her sister, forgetting herself in her grief.
Father looked at her strangely. “Gods, “ he swore softly, “out of the mouth of babes...” He shouted for Septa Mordane.
-A Song of Ice and Fire: Book One - A Game of Thrones, Chapter Fourty-Four (Sansa III).

There's no way that Pycelle could have foreseen that epiphany.

1

It is true that Pycelle knew the parentage of the royal children but there is no evidence that he knew it was a plot of Little Finger nor who had actually done the deed. From his point of view, he was just helping who he thought was the real murderer (Cersei). The short answer is that he is not that smart and is just a pawn. There is evidence that he is not astute in the game of thrones. In Clash he falls easily into the trust trap Tyrion creates to find out who can be trusted. He later falls asleep during the wedding of Joffrey. He is just lucky to have survived this long

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