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Illyrio used to be a poor Bravo, but in Pentos he met the eunuch Varys. and they started a business where Varys would steal objects from lesser thieves and Illyrio would get the objects back for their original owners for a small fee. Soon, every man and woman in Pentos who ever had valuables stolen from them all knew who to ask to get their valuables back. In addition, the thieves in Pentos soon began to seek Illyrio and Varys out, half to try (and failing) to kill them, the other half to sell them the objects they stole in order to prevent Varys from stealing them back. Varys and Illyrio grew very rich, allowing Illyrio to marry the daughter of a cousin of the Prince of Pentos. After her death Illyrio married again, to a Lyseni pillow-house worker, Serra. She died when a plague swept through Pentos. Illyrio keeps her portrait and hands.
Viserys Targaryen and Daenerys Targaryen are kept in Illyrio's Manse, Illyrio apparently intending to restore them to power. At first he thought of killing Viserys and claim Daenerys as a wife, but he soon dismissed the idea soon as he believed she was too timid and frightened and that having sex with her would have been boring. He claims his motives are financial, intending to be made Master of Coin under Viserys. Illyrio arranges Daenerys marriage to Khal Drogo, leader of the largest Khalasar, which will be used to help restore the Targaryens to power. Illyrio gifts Daenerys with three dragon eggs.
Illyrio meets Varys in King's Landing, who tells him he needs more "little birds" (trained children with their tongues cut out). They are overheard by Arya Stark, who doesn't understand what they are saying.
Viserys is later killed by Drogo, who later dies himself. On his funeral pyre the dragon eggs hatch, restoring dragons to the world.
With her three dragons Daenerys travels to Qarth. When she tries to leave the city she is met by men sent by Illyrio, the eunuch Strong Belwas and Arstan Whitebeard (really the Kingsguard Barristan Selmy, who was dismissed on the accession of Joffrey Baratheon). Illyrio intends for Daenerys to come to him, having sent her three ships, but she instead decides to go to Slaver's Bay, where she fights the Masters of all three cities, eventually taking control of Meereen.
When Tyrion Lannister is convicted of poisoning Joffrey he is broken out by Varys and smuggled to Illyrio's Manse. Illyrio tells Tyrion he is working for a Targaryen restoration and will help Tyrion become Lord of Casterly Rock, which Tyrion regards as his birthright. Tyrion suspects Illyrio has ulterior motives in helping the Targaryens, other then just becoming Master of Coin. Tyrion is told he will meet the Golden Company, the best sellsword company. Tyrion is suspicious of this, as the Golden Company was founded to fight the Targaryens in favor of the Blackfyres, a legitimized bastard cadet branch of Targaryens. Illyrio brushes this away, and states the Blackfyres are extinct in the male line.
On the pole-boat travelling to Volantis, Tyrion finds out the boy travelling with them, "Young Griff", is apparently Aegon Targaryen, son of Rhaegar Targaryen, and their supposed father "Old Griff" really Jon Conninton, the exiled Lord of Griffin's Roost and a friend of Rhaegar. Illyrio intended for Aegon to marry Daenerys and they would rule the Seven Kingdoms together.
In Volantis Aegon and Jon meet the Golden Company. Its commanders are annoyed at Illyrio's continually changing plans and Daenerys not complying, meaning they have had to break a contract and march on Volantis, and are delaying on a highly profitable contract with Volantis. Inspired by a conversation Tyrion had with him during a cyvasse game, saying the Seven Kingdoms would never be more ripe for conquest, Aegon tells the Golden Company that instead of going east to Slaver's Bay they should go west to Westeros, and Daenerys can come to them. The Golden Company agree and travel to Westeros.
- It is theorized Illyrio Mopatis may be the father of the supposed Aegon Targaryen, via his second wife Serra, who had Valyrian features like Aegon. The statue of a younger Illyrio in his courtyard has similarities to Aegon's appearance. Tyrion thinks that Illyrio has some ulterior motive in aiding the Targaryen restoration.
- In line with the theory that Aegon is a female-line Blackfyre is Illyrio saying the Blackfyres have ended in the male line, implying their are female-line descendants. Serra may have been a Blackfyre descendant, her Valyrian features being evidence of this.