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In season 1, there is a rather cryptic conversation between what appears to be Illyrio and Varys, that Arya overhears after she chases a cat downstairs.

In the conversation a plot is mentioned (A murder?).

I never understood the underlying dynamic here, other that creating a theme of distrust and intrigue.

So what's going on? Who is plotting for what?

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I assume you are talking about this scene: – TLP Jul 24 '14 at 2:47
up vote 8 down vote accepted

The scene, I assume is this one:

The conversation goes like this:

Varys: He's found one bastard already. He has the book. The rest will come.
Illyrio Mopatis: And when he knows the truth, what will he do?
Varys: The gods alone know. The fools tried to kill his son. What's worse, they botched it. The wolf and the lion will be at each other's throats. We will be at war soon, my friend.
Illyrio Mopatis: What good is war now? We're not ready. If one Hand can die, why not a second?
Varys: This Hand is not the other.
Illyrio Mopatis: We need time. Khal Drogo will not make his move until his son is born. You know how these savages are.
Varys: "Delay," you say. "Move fast, " I reply. This is no longer a game for two players.
Illyrio Mopatis: It never was.

The two men are Varys and Illyrio Mopatis.

They are talking about Ned finding one of King Robert's bastards, Gendry, I assume. The book is the book that the murdered Jon Arryn reportedly was reading when he died, namely The Lineages and Histories of the Great Houses of the Seven Kingdoms. In that book, Ned can later see that in all previous marriages between Lannister and Baratheon, the children have had black hair, whereas all three of Cersei Lannister's and Robert's children are blond -- a sign that Robert is not the father.

They are talking about that someone tried to kill Bran, but they do not know who (we know it was Joffrey). They state that this will soon lead to Lannister and Stark clashing, which will lead to war. If Robert had been alive, this would have been very bad for house Lannister. Illyrio suggests killing Ned, but Varys declines, for some reason that we do not really know. Perhaps he likes Ned, or thinks he has some other redeeming value. If indeed (spoiler ADWD)

Aegon VI Targaryen

is the real deal, they might have some use of Ned, because he knew some of the people involved, which could support this person.

Of course, we know about Khal Drogo and Daenerys, and Viserys' plan to use Drogo's huge khalasar to invade Westeros. (My overly detailed analysis of their game plan is here. TL;DR: Viserys was being set up as a badguy.) It is interesting to note that they are not talking about Dany here, it is assumed later on that she was not originally part of their plan.

The rest of the conversation is vague. Perhaps the "two players" refer to Varys and Illyrio, or perhaps it refers to two factions, and this implies that a third faction (or more) has entered the game.

The game is, of course, The Game of Thrones, the struggle for control over the Iron Throne.

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Illyrio is clearly talking about Dany making her return; he's seeing the inevitable Stark/Lannister/Baratheon clash brewing and wants to stop it until Dany is ready to come back with her army. He wants to kill Ned to stop him from revealing what he knows to Robert. Varys seems to recognize that the war will be far more chaotic than Illyrio realizes, and will leave Westeros ripe for Dany and/or Argon to step in and take it, even years later, and wants to start letting the major players kill each other off now. – KutuluMike Jul 24 '14 at 13:09
Correction - the "fools" who tried to kill Bran in this case are Cersei & Jaime, not Joffrey. – Omegacron Jul 24 '14 at 19:52
@MichaelEdenfield Dany's dragons had not been born at this time. The deal Illyrio made was with Viserys: He was the one that was supposed to get a crown in return for giving his sister to Khal Drogo in marriage. This is the original deal. As Illyrio tells Tyrion in ADWD, he did not even expect Dany to survive life in the khalasar. They later changed the deal when Viserys was killed, and Dany's dragons hatched, but that point is not now. – TLP Jul 24 '14 at 21:31
@Omegacron Yes and no. Jaime shoved Bran from a window, but the assassination Varys is talking about is the one that Lady Catelyn came to King's Landing to report to Ned, the one with the valyrian steel dagger. We later learn, first in a Tyrion POV and later in a Jaime POV that Joffrey was the one who sent the man with the King's own dagger to slit Bran's throat. – TLP Jul 24 '14 at 21:34
This is such a good answer! – Mooz Sep 26 '14 at 5:15

We find out their endgame much later in A Dance With Dragons (and perhaps in season 5 of the TV series):

Varys supposedly saved Aegon Targaryen, the second child and only son of Prince Rhaegar Targaryen and Elia Martell. They arranged for him to be raised in Essos, have prepared him for rule, and are conspiring to put him back on the Iron Throne.

Varys sums it up nicely at the end of ADWD:

Aegon has been shaped for rule before he could walk. He has been trained in arms, as befits a knight to be, but that was not the end of his education. He reads and writes, he speaks several tongues, he has studied history and law and poetry. A septa has instructed him in the mysteries of the Faith since he was old enough to understand them. He has lived with fisherfolk, worked with his hands, swum in rivers and mended nets and learned to wash his own clothes at need. He can fish and cook and bind up a wound, he knows what it is like to be hungry, to be hunted, to be afraid. Tommen has been taught that kingship is his right. Aegon knows kingship is his duty, that a king must put his people first, and live and rule for them.

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