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
Illyrio Mopatis: And when he knows the truth, what will he
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.
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.
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.