Why did Varys leave with Tyrion? The reason surfaces only after the crate reaches Pentos

At the end of "The Children," the season 4 finale that aired on June 15, 2014, Jaime frees Tyrion from his cell and Varys seals him into a wooden crate bound for Essos. Watch the scene closely: Varys hands the crate off and turns back toward the Red Keep. He fully intends to stay in King's Landing.

Then the bells start ringing, and he sits down next to the crate instead.

The bells were the immediate reason

Between his cell and the ship, Tyrion detoured through the Tower of the Hand and put two crossbow bolts into his father on the privy. Those bells meant Tywin Lannister's body had been found — and that the search for whoever freed the prisoner would start immediately. Varys, whose entire career rests on never being the one holding the evidence, did the arithmetic on the dock and boarded.

Self-preservation got Varys onto the ship. It does not explain why he then spent a season escorting a fugitive across a continent.

What he admits in Pentos

That explanation arrives in the season 5 premiere, "The Wars to Come" (April 12, 2015), when the crate is finally pried open at the mansion of Illyrio Mopatis in Pentos — after a crossing Tyrion describes in vivid detail involving the crate's air holes. Varys reveals the actual scope of the operation:

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• The conspiracy is old. He and Illyrio have been working toward a Targaryen restoration for years — it predates everything viewers saw in season 1.
• The rescue was a recruitment. Varys didn't save Tyrion out of sentiment; he wants his political mind in service of the cause.
• The candidate isn't a king. Varys describes the ruler Westeros needs — beloved, feared, well-armed, correctly surnamed — and lets Tyrion assume he means a man.

"Who said anything about him?" Varys replies, and the destination becomes Daenerys Targaryen in Meereen.

Tyrion agrees, on the condition that he can drink himself across Essos. The plan promptly falls apart in Volantis, where Jorah Mormont kidnaps Tyrion out of a brothel, and Varys doesn't resurface until the season 5 finale in Meereen.

The books do this completely differently

In A Dance with Dragons, Varys never leaves King's Landing. Tyrion is smuggled out through Jaime and Varys's arrangements, but he crosses alone and is received in Pentos by Illyrio in person. Varys stays behind, vanishes into the walls of the Red Keep, and reappears in the novel's epilogue to remove Kevan Lannister and Grand Maester Pycelle from the board.

The bigger divergence is the cause itself. In the novels, the Varys-Illyrio project centers on Young Griff — a teenager presented as Aegon Targaryen, Rhaegar's supposedly surviving son — whom the show cut entirely. Screen-Varys absorbed Illyrio's travel itinerary and had his cause rewritten to point at Daenerys from the start.

For the record: the man who left King's Landing to install a ruler with "the right family name" was executed in season 8 by exactly that family name, for shopping around a different Targaryen. The strategy never changed. The candidates kept failing the interview.

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