As the TT thinks more on top of the crest, the full moon comes out, the creatures go into buildings, and he decides to find someplace to sleep. He looks at the garden with the White Sphinx and is shocked to find the Time Machine is gone. Scared he may be stranded in the future, he runs down to the garden. The one thought that consoles him is that without the levers, the Time Machine is inoperable. In a panic, he runs around the garden looking for the machine, startling what he takes for a small deer in the dim light. He goes into the great stone building from before, lights a match, and finds a second great hall inside it where many of the creatures sleep.
Several of the creatures awaken when the TT cries out for his Time Machine. He calms down and goes outside again, only to hear their "cries of terror" as they run about. He gropes about in the darkness for the Time Machine, "touching strange creatures in the shadows," until he falls asleep on the ground and wakes up to the new day. He resolves to make the best of his situation and possibly build a new machine, but first he will search for the old one. Interrogations of the creatures are fruitless, but he finds hints that the machine was dragged into the hollow bronze pedestal under the White Sphinx, as well as nearby footprints of a creature he imagines might be a sloth. However, he does not know how to open the pedestal, and when he indicates to the some of the creatures that he wishes to open it, they seem deeply offended and leave. He bangs against the pedestal and believes he hears something move inside. After banging against it with a pebble, he beseeches himself to be patient.
Over the next couple of days, the TT learns some more of the creatures' simple language and tries to forget about his missing Time Machine until he has gained enough knowledge to recover it. The environment proves uniformly beautiful, but the deep, circular wells continue to puzzle him, as does the vacuum they produce and the thudding sound from below. He connects the presence of the wells with the tall towers spread about and concludes that there is a subterranean ventilation system, an idea that will prove to be wrong. He admits he learns little about transportation and other features of the society, other than receiving a "general impression of automatic organization." The absence of any elderly or ill creatures perplexes him, as does the absence of any burial grounds or tombs. Though he cannot believe the society is fully automatic, he cannot find any other explanations.
On his third day, the TT saves a young female creature from drowning in the shallow river. Later, she presents him with a garland of flowers. Her name is Weena, and the TT explains it was the beginning of a "queer friendship which lasted a week, and which ended--as I will tell you!" Weena follows him around like a puppy, and she is distressed when she cannot keep up with his explorations and is left behind. The TT explains that he did not know until it was too late what he had "inflicted upon her" each time he left her behind, nor did he understand what she meant to him. He learns that her only fear is of the dark, and that after dark, the creatures sleep only inside in groups. Still, the TT continues to sleep away from the groups. Weena eventually sleeps next to the TT.
The TT resumes talking about the night before he rescued Weena. He awakes at dawn, and twice sees white, ape-like creatures running alone up a hill, and once sees several of them carrying a dark body. Once the sun rises, he sees them no more and wonders if they were ghosts. Though the rescue of Weena that day makes him forget them, he says they would soon take a "far deadlier possession of my mind." On his fourth morning, while seeking shelter from the heat in one of the ruins, the TT finds a dark, narrow gallery. Entering it, he comes across a pair of eyes watching him in the darkness. He speaks and touches something soft, then sees a small, white ape-like creature run behind him in the sunlit space. He follows it into a second ruin where he finds a well. Lighting a match, he peers inside it and sees the creature climbing down metal foot and hand rests on the wall.
The TT realizes that man has evolved into two distinct animals, the "Upperworld" creatures and the nocturnal ones below. Wondering what the relationships is between the two, he resolves to descend into the well, though he is afraid to do so. Two of the Upperworld creatures are distressed to find him looking in the well, and leave him. He comes up with a new theory of how their world operates: the new species he has found are subterranean and live in tunnels ventilated by the towers and wells, and work to ensure the functioning of the Upperworld. He believes the human race has split as a result of the widening gap between the "Capitalist and the Labourer," and that the poor have been increasingly relegated to underground areas, while the rich have remained on the surface. The lack of interaction between the "Have-nots" (the poor workers) and the "Haves" (the rich) has cut down interbreeding and created two distinct species who have adapted to their own environments. Nevertheless, he believes that the species are equally happy. He believes humanity has not triumphed merely over nature, but over "Nature and the fellow-man." The TT explains that he is not sure if this is the correct explanation, but it seems the most plausible one to him. He wonders why the Morlocks--the name of the Underworld creatures--have taken his Time Machine, and why the Eloi--the Upperworld creatures--cannot return it to him, if they are the masters, and why they are afraid of the dark. Weena refuses to answer his questions, even crying.
The TT finally receives enough clues in this chapter to make some more grounded theories. The future is not a Communist state, as he previously believed, but an excessively capitalist one that has completely divided the Haves and the Have-nots. Moreover, the TT sees a natural integration of capitalism and evolution in human history. The differences between the rich and poor in his contemporary England, especially in places of habitation, have led to the physical evolution of two distinct species.
We may read this evolution as a harsh critique of capitalism; though the TT believes the two species are equally happy, we have already seen enough defects just in the Eloi--notably their weakness and stupidity--that indicate Wells's disapproval of the capitalist evolution. The Eloi (their name even sounds like "elite") are representatives of the upper-class of Victorian England, childishly leading lives of luxury, while the Morlocks (their name is fittingly crude) are projections of England's oppressed workers, toiling underground to provide for their masters. But there is evidence that the Eloi fear the Morlocks, and that they cannot get the Time Machine back from them suggests there is more to their relationship than the TT initially assumes.
This chapter also details the TT's scientific method in a variety of settings. Each time, he calmly devises an experiment with a possible hypothesis in mind, runs "tests" (such as throwing a piece of paper into the well), refines his ideas, and settles on a conclusion. However, he admits that nearly all of his conclusions turn out to be wrong.
Finally, the TT gains an ally in Weena. The TT indicates that something bad will happen to her, but for now she is interesting as a representative of femininity in the future. Though the TT has previously labeled the sexes indistinct, Weena seems in love with the TT. He grows attached to her, as well, but they seem to fit into contemporary gender stereotypes--he as the strong male, she as the dependent female.
The TT is frightened by his discovery of the Morlocks, and cannot muster the courage to go underground and confront them about his stolen Time Machine. Instead, he explores the Upperworld more, one day happening upon a huge green structure which he calls the Palace of Green Porcelain. Finally he decides to descend into the well, an action that greatly distresses Weena.
He climbs down the well as the thudding sound of some machine grows louder in the dark. He rests in a tunnel, and is woken by three Morlocks. They flee when he lights a match, and the TT cannot communicate with them as they speak a different language from the Eloi. He finds his way into a large, dark, machine-filled cavern where the Morlocks eat meat. Running low on matches, he does not light another, and soon feels the Morlocks groping him. He shouts at them, then lights a succession of matches as he escapes. He nearly faints as he ascends into the Upperworld, where Weena kisses him. He explains he was "insensible" for a brief time.
This short chapter sets the stage for the TT's inevitable confrontation with the Morlocks. He verifies that there are, indeed, machines underground which the Morlocks tend to, though it is not clear for what purpose. He also learns that meat exists in the future, and that the Morlocks eat it, though he does not know what kind of meat it is.
We also see how unequipped the TT is for the Underworld of the Morlocks. He has difficulty climbing up and down their shafts, and he requires a match to navigate in the darkness. By contrast, he is much at home in the world of the Eloi, even fitter than they are. It is understandable that the TT, a member of the Victorian ruling class, would have more in common with the elite Eloi than with the toiling Morlocks.