Ned Malone and Lord John Roxton retire to Lord John's rooms to discuss the upcoming expedition. Lord John, who is an accomplished sportsman, has his wall full of trophies and the trappings of a man who is an adventurer.

He asks Ned if he will do him a favor, which is to help him feed his upstairs neighbor who taken ill, after being drunk for days. The problem is the man is an accomplished marksman and he has vowed to kill anyone who tries to feed him. Ned, while not happy about the situation, agrees to help Lord John save his neighbor. Lord John then lets Ned know he was only testing him, to see if he had the courage necessary for the adventure they are about to embark upon. Lord John feels the success of the expedition rests with him and Ned, because he feels Professor Summerlee will be more of a hindrance than a help.

Lord John is also concerned with Ned's ability to shoot a rifle, because in the jungles of South America the ability to shoot straight can mean the difference between life and death. Ned tells him he is an average shot, which in Lord John's estimation is not good enough. He loans Ned one of his rifles for the journey.

They decide to book passage on a boat for South America and leave the Wednesday of the following week. They speak of how neither one of them know Professor Challenger well, but they both believe he may be telling the truth. Lord John believes him, because he has traveled extensively in South America and can fathom there being such a place as Challenger describes.

After his meeting with Lord John, Ned meets with his editor, McArdle, and the two decide to talk to the chief of the paper, Sir George Beaumont, about Ned's assignment. Ned will write letters to McArdle, which will be published when they are given permission by Challenger.

As the three men are boarding the boat Challenger meets them with instructions to open an envelope containing the location of the animals, after they reach a town called Manaos. He also tells Ned he may print whatever he likes about the expedition, as long as he does not give away where the men are on the continent.

The three men arrive in South America and travel to the town of Manaos. They have hired some men to aid them in their journey, they are Zambo, Gomez, Manuel, Mojo, Jose, and Fernando. At the appointed hour the men open the envelope Challenger gave them as they boarded the ship. Inside the envelope is a blank sheet of paper; the men are confused and Mr. Summerlee is angry, as he feels the trip has been a colossal waste of time. Just as they are discussing what this means, Challenger appears at the door to their room. He has come by boat to take command of the expedition. He has also made arrangements for the same two Indians, who went with him to the secret place the first time, to join them now. He has hired a boat, the Esmeralda, to take them down the Amazon.

On August 6 the men must disembark from the Esmeralda and use canoes to go deeper into the area around the river. The men are now traversing the smaller rivers which sprout from the Amazon. Professor Challenger and Professor Summerlee are at odds, as they argue about every subject of conversation.

As they move further down the river the men begin to hear the beat of drums. It is the Indian tribes watching the men's progress down the river. They are waiting for an opportunity to attack; the drumbeats mean "We will kill you if we can".

After a few days, Challenger sees his first marker that they are on the correct trail, it is an Assai palm tree. He now feels more confident that they are on the correct course. Three days later they push through to the land that is forbidden to the Indians, the land of the Curupuri.

They reach an area where they can no longer use the canoes and everyone must help carry the provisions. It is here Professor Summerlee challenges Professor Challenger's authority to lead the group. He tells him he is, after all, on trial for his discovery and so should not be telling the others what to do. Lord John and Ned calm the two men and the expedition continues on its way.

Ten days later as the men are walking Professor Challenger spots a large flying animal. He tells Summerlee it is a pterodactyl, but Summerlee is certain it is a stork. Lord John tells Ned it is unlike any animal he has ever seen.

The men are now about seven miles away from the plateau Challenger discovered, which he says contains the prehistoric animals.

The men have sailed to South America, traveled down the Amazon, and trekked to an area very near the plateau Challenger found. The two professors have not gotten along, but Lord John and Ned have done their best to keep harmony among the group.