Destruction of the pirate fleet

"There's nothing that can hold against the armada, not with the Flying Dutchman at the lead."

- Mercer to Cutler Beckett

The Destruction of the pirate fleet was a minor battle between the Flying Dutchman operating for the East India Trading Company and a small fleet of pirate ships, that convinced Lord Beckett that the Dutchman needed to be under tighter control in order for it to be used as an integrated part of his armada.

Discussion aboard the Endeavour
"The Brethren know they face extinction. All that remains is where they make their final stand."

- Beckett on the destruction of the small Brethren Court fleet

On board the HMS Endeavour, Mercer conversed with Cutler Beckett over the discovery of a Piece of eight coin. (This coin is most likely the one Sao Feng was given by Hector Barbossa.) Mercer had just returned from the Singapore and had presented it as a tidbit of information. Around the same time, James Norrington entered into the main cabin, and Beckett represented his sword to him, and proclaimed the Brethren Court on the verge of extinction.

The Battle
"Bloody Hell, there's nothing left."

- Cutler Beckett upon arriving at the scene of the battle.



Around that time, a small pirate fleet was on the way to Shipwreck Island in order to join the Brethren Court meeting, when the Flying Dutchman rose out from behind them, opened all of its gun ports, including the Chase guns and opened fire. The pirates were surprised by this attack and before they could return fire, the Flying Dutchman sailed between them firing in all directions. The captains of the ships were powerless to fight back, and the Dutchman obliterated all the ships in its path. Due to Jones's temperamental frustration about being under Beckett’s command, all aboard were killed.

Confrontations
"The Dutchman sails as its captain commands." "And its captain is to sail it as commanded! I would have thought you learned that when I ordered you to kill your pet. This is no longer your world, Jones. The immaterial has become...immaterial."

- Davy Jones and Cutler Beckett on Jones's Freedom.



However, when Lord Cutler Beckett arrived at the site, he became angry since he wanted prisoners in order to question them about the pirate lords. Thus, so he ordered the transfer of the heart of Davy Jones from the Endeavor to the Flying Dutchman in order to ensure Jones's good behavior. Jones was in a foul mood, as he had just shed a tear for his lost love Calypso, but Beckett reminded Jones that he had ordered him to kill his pet, and then stationed a large group of East India Trading Company Marines led by James Norrington aboard the ship.

Aftermath
"Signal the Dutchman to track down Sao Feng"

- Beckett after the Skirmish off of the Kraken Island

The destruction of the fleet struck fear into the pirates' hearts, and with the Heart of Davy Jones on board, Beckett was much more confident in his ordering of the Dutchman. Thus, when Beckett had some trouble later with Sao Feng, he did not hesitate to call on the Dutchman to crush the opposition.

Source
Pirates of the Caribbean: At World's End