According to Caesar, Pompey went from Mytilene to Cilicia and Cyprus. He took funds from the tax collectors, borrowed money to hire soldiers, and armed 2,000 men. He boarded a ship with many bronze coins. Pompey set sail from Cyprus with warships and merchant ships. He heard that Ptolemy was in Pelusium with an army and that he was at war with his sister Cleopatra VII, whom he had deposed. The camps of the opposing forces were close, thus Pompey sent a messenger to announce his arrival to Ptolemy and to request his aid.

Potheinus the eunuch, who was the boy king's regent, held a council with Theodotus of Chios, the king's tutor and Achillas, the head of the army, amongst others. According to Plutarch, some advised driving Pompey away, and others welcoming him. Theodotus argued that neither option was safe: if welcomed, Pompey would become a master and Caesar an enemy, while, if turned away, Pompey would blame the Egyptians for rejecting him and Caesar for making him continue his pursuit. Instead, assassinating Pompey would eliminate fear of him and gratify Caesar.

On 28 September, Achillas went to Pompey's ship on a fishing boat together with Lucius Septimius, who had once been one of Pompey's officers, and a third assassin, Savius. The lack of friendliness on the boat prompted Pompey to tell Septimius that he was an old comrade, the latter merely nodding. He thrust a sword into Pompey, and then Achillas and Savius stabbed him with daggers. Pompey's head was severed, and his unclothed body was thrown into the sea.

When Caesar arrived in Egypt a few days later, he was appalled. He turned away, loathing the man who brought Pompey's head. When Caesar was given Pompey's seal ring, he cried.Theodotus left Egypt and escaped Caesar's revenge. Pompey's remains were taken to Cornelia, who gave them burial at his Alban villa.