After their adventures in the South Sea Islands, Jack Martin, Ralph Rover, and Peterkin Gay go their separate ways. Six years later, Ralph (again the narrator), living on his father's inheritance on England's west coast and occupying himself as a naturalist, is visited by Peterkin, whose "weather-beaten though ruddy countenance" he does not recognize. Peterkin, who has stayed in touch with Jack, has hunted and killed every animal on Earth except for the gorilla and now comes to Ralph to entice him on a new adventure. After Peterkin writes him a letter, Jack joins the two, and they leave for Africa.
The three pick up a native guide and attend an elephant hunt. All kinds of animals are shot, killed, eaten, and stuffed, and the action is interspersed with sometimes serious, sometimes jocular conversation. Ralph theorizes at length on "muffs", which he defines as boys who are too gentle and mild, and should be made to undergo physically challenging training. Trading habits in this part of Africa are discussed: trade between the jungle and the coast is done via all the intermediary tribes, a cumbersome and expensive way of doing business. The trader who explains this to Ralph is a friend of missionary efforts: when the natives are ruled by their "abominable superstitions", they become "incarnate fiends, and commit deeds of cruelty that make one's blood run cold to think of". In addition, the trader argues that missionary work and trade should join to improve the fate of Africa: "No good will ever be done in this land, to any great extent, until traders and missionaries go hand in hand into the interior, and the system of trade is entirely remodelled".
In the village of King Jambai, the hunters are well received (boiled elephant foot is served and judged delicious), but problems arise when a young woman, betrothed to Makarooroo, their English-speaking guide, is judged by the village's "fetishman" to be responsible for an illness of the king's, and she is to die. The hunters help spring her from her jail, and in the melee that accompanies their escape two natives are killed: Jack trips one who falls to an accidental death in a pit, and Makarooroo kills another. They hide the woman a few days later with Mbango, the king of another tribe. Peterkin shoots an elephant, but a further hunting adventure goes badly for Jack, who went giraffe hunting by himself but is seriously injured by a rhinoceros. To recuperate the hunters spend a few weeks in the village of another tribe, ruled by a relative of King Jambai.
The plot for the second half of the book involves a slave trader, whom the three hunters and their guide pursue for weeks to prevent the trader and his gang from taking over and enslaving Mbango's people. They are too late, and Makarooroo's fiance is among the captured. When the trader attacks Jambai's village the three organize the defenses and successfully defeat the attackers. It is a relatively bloodless affair, since Jack has ensured that the first volley from Jambai's riflemen consists of wadded paper, intended to scare off the attackers without killing them. In addition, Peterkin dresses up in a colorful outfit and stands on top of a hill, screaming and setting off fireworks. However, when Ralph attacks the trader's camp, he manages to scare off the now-liberated slaves, and another weeks-long pursuit ends with the happy reunion of Makarooroo and his fiance, who head down to the (Christianized) coast to get married. After the three take receipt of their stuffed trophies, intended for British museums and schools, they head home, with Ralph and Peterkin saying farewell:
"Farewell," said I, as we leaned over the vessel's side and gazed sadly at the receding shore --- "farewell to you, kind missionaries and faithful negro friends."
"Ay," added Peterkin, with a deep sigh, "and fare-you-well, ye monstrous apes; gorillas, fare-you-well!"

Question: What do the men plan to do with the animals they killed?
Answer: Give them to British schools and museums.