On June 4, 1646, a new Ottoman armada of 60 galleys and four galleasses emerged from Istanbul, reinforced by Barbary states, and sailed to Chania.

Soon after the conquest of Chania, the most prominent men had written to Hussein Pasha that they were ready to submit to the Sultan since they could no longer expect anything from Venice, and the people were fed up with the Venetian government, which they hated and which could not even provide them with protection.

A Venetian commander, Cormaro, who had tried to maintain some semblance of order among the retreating, received a fatal bullet wound amid the chaos and died on the spot.

Not only were the walls almost destroyed in a few days by the Ottoman cannon fire, but inside the castle, the plague was wreaking havoc.

Hussein Pasha, whose troops were likewise greatly weakened by the plague, immediately stopped firing.