Upon further inspection of the ship they’ve sighted, they spy a black flag sailing from the mast and realize it may be a pirate ship. Desiring to conceal their presence, they quickly attempt to camouflage the evidence that anyone is currently living on the island while also gathering their weapons in Granite House. Dropping anchor in the harbor, the ship fires a cannon shot, indicating their intention to stay in place and possibly come ashore. By now, it is night.

The men are anxious to observe the actions of the ship and those aboard and discuss their options. Ayrton volunteers to swim out to the ship to ascertain the nature and number of the crew. Cyrus objects to this as he doesn’t want Ayrton putting his life in danger, but Ayrton insists: “Mr. Cyrus, I’m begging you, as a favor. This might help to redeem me in my own eyes!” (510). Pencroff accompanies Ayrton to the shoreline in case they encounter anyone on the way there who may have already landed.

Finally making it to the ship, Ayrton discovers that it is filled with escaped convicts from Norfolk, that the ship’s name is the Speedy, and that the crew of English prisoners is captained by an old acquaintance of Ayrton’s, Bob Harvey. In time, Ayrton discovers that the pirates have arrived here purely by chance but that they have plans to make it their home port and make use of the island’s resources. Ayrton proceeds to sneak onto the ship once the men have fallen asleep, discovering more details about how they are armed and how many of them there are, counting close to 50 men.

In an act of courage, Ayrton decides to sacrifice his own life for the sake of his companions. He attempts to find the powder magazine to blow it up and destroy the ship and the whole pirate crew. Before he can do so, however, he is caught by Bob Harvey. In the act of escaping the pirates, he is wounded in the shoulder. He makes it back to land, and he and Pencroff relate all the details to the men later that evening.

The next morning, Cyrus hatches a plan: They will split into three groups to ward off the pirates, attempting to trick their assailants into believing that the island is populated with far more people than it is. Set in place, the men watch a boat set out from the larger ship with seven men. As the boat approaches, the men manage to gun down four of them while the large ship proceeds to send cannonballs toward the island as retaliation. The remaining three men return to their ship, but two more boats launch back out into the water with three times the number of pirates.

Fighting the pirates as they retreat back to Granite House, the men watch as the large ship makes its way closer and closer to a position where it can fire its cannons onto the island. Spying the suspicious camouflage with which the men attempted to hide their home, the pirates fire cannonballs at Granite House and begin to destroy it.

All at once, however, something wholly unexpected occurs: “A great column of water had lifted the helpless brig high above the surface of the sea. All at once the ship broke in two, and in less than ten seconds it had sunk, with all its felonious crew!” (535). Completely miraculously, the men are saved.

Making their way down to the shore to investigate, the men gather much of the remaining pieces of the ship that are salvageable and may be useful to them in the future. They discuss the curious nature of what has just occurred; nobody is able to offer a logical explanation.

At low tide, they venture further out to explore the wreck, aghast at what they find:

The copper sheath and the planking had disappeared, no doubt vaporized in the blast; but, more than this, the very ribbing of the hull, the iron bolts, and the treenails had vanished without a trace […] and the keel itself had split from one end to the other, torn from the keelson in several places (542).

The rest of the ship is unsalvageable.

They are able to rescue a good number of goods from the ship, including a large number of powder kegs that are untouched, proving that the ship did not explode on its own and deepening the mystery. Over the next three days, the men extract all they can from the ship, and on the third night, a storm kicks up and completely sinks the remains of the wreck, leaving no trace. One month later, however, Neb discovers the remains of a sea mine, which the men determine must have been the cause of the ship’s destruction.

The presence of the mine certainly explains the explosion but does not explain why a sea mine was off the coast of a previously undiscovered island. Cyrus concludes, “[W]e can no longer doubt the presence of some mysterious being on these shores, perhaps a castaway like ourselves, stranded here as we are…Who is this benevolent stranger who has so generously intervened in so many varied circumstances? I cannot imagine” (549-50). All agree and are determined to search for the seemingly omnipotent individual that has been the cause of much of their fortune on the island thus far.

In the meantime, they take pains to install the cannons from the ship in various strategic locations for their own defense and keep their eyes out for the six remaining pirate castaways that landed on the shore before the explosion, escaping into the jungle without a trace. The men increase the defenses of Granite House and check on the safety of the Bonadventure, which Pencroff and Harbert suspect may have been tampered with. There is no evidence, however, of sabotage.

Attempting to contact Ayrton down at the sheepfold using the telegraph, they are surprised to receive no response. Anxious about Ayrton’s safety, they set out at once, completely armed, and discover along the way that the telegraph line has been tampered with. They race to the sheepfold when all of a sudden, a gunshot is heard. Harbert collapses to the ground, struck by a bullet.

Gathering the injured Harbert up, Cyrus spies one of the escaped pirates and kills him with a dagger to the heart. After striking down the pirate, Cyrus returns as the men try to save Harbert’s life, availing themselves greatly of Gideon’s rudimentary knowledge of medical science. With still no sign of Ayrton, they send Top back to Neb with a message about their current situation.

The pirates continue to remain near the sheepfold, and with Ayrton’s continued absence, the men are convinced that he must have met his end at the hands of their enemies. Finally, 10 days after being shot, Harbert demonstrates marked improvement, even being capable of conversation. Meanwhile, stuck in the small building and without any new thought of how to escape and overcome their adversaries, Cyrus begins to wonder if their luck has finally run out.

As Harbert recovers, the men spend their days waiting and watching. On one occasion, Gideon chooses to take a walk around the small perimeter of the area, taking Top. Top picks up a scent and manages to sniff out a shredded piece of Ayrton’s jacket. The men renew their hope that they might be reunited, but bad news arrives almost as suddenly: The orangutan Joop arrives at the sheepfold with a message from Neb, notifying them that the plateau has been invaded. They decide to leave at once, transporting Harbert—still only half recovered—in a handcart to ease his journey.

They arrive at Granite House and discover that the pirates set fire to the mill and destroyed a vast portion of their crops. Harbert has fallen into a worse state than ever before and is showing signs of real danger. The men try to find natural remedies in the forest, but Harbert continues to deteriorate with fever and delirium. The morning after a dreadful night, they awaken to a surprise gift on the table by Harbert’s bedside: a box of quinine sulfate, the precise remedy they need to cure Harbert’s fever and illness.