As the Time Traveller is reflecting on his theories, night begins to fall. He heads back to his time Machine. As he approaches the spot from a distance, the machine appears to be gone, and he breaks into a desperate run. It is gone. He is sure that no one travelled in time, because he took the levers, but someone has obviously moved it in space. He believes that the creatures he has encountered so far are too weak to move the machine. He goes into a frenzy, running around the Sphinx statue, where he startles a white creature that runs away. He goes into the hall and wakes the sleeping creatures, demanding his time machine in a gruff manner, which scares the creatures. The narrator calms down and tries to reason out where his machine might be and how he can get it back.
That morning, the traveller decides that since he was only away from the machine for a short time it can't have gone very far. He concludes that the machine must be hidden in the immense pedestal of the sphinx statue. He tries to open the pedestal's panels with a rock, but does not succeed. When he asks the creatures how to open it, they react with shock and disgust. He decides that he must be patient, and that it would be a good idea to get to know the creatures better. He learns more of their language and explores the area. He pays more attention to the wells dotting the landscape, and notes that air seems to be sucked down into them. He can hear the dull sound of machines coming from below.
He begins to reconsider his theory that the creatures come from a decadent, automated civilization, for he notices that there are only buildings, and that the clothes of the creatures must be made somewhere. He also doesn't understand the strange wells, or how his time machine disappeared.
Meanwhile, the Time Traveller rescues one of the creatures from drowning in the river, which has shifted a mile or so from the bed of the Thames. Her name is Weena, and she seems like an affectionate, precocious child to him. She greets him when he returns to the area of the white sphinx statue, making it feel like home. Like the other creatures, she is very afraid of the dark. Her fellow creatures sleep in great clumps in the halls of the buildings, and she is very reluctant to let the narrator sleep elsewhere. One morning, the narrator wakes up at dawn and goes out on the porch of one of the buildings. He imagines he sees white figures moving around in the dull pre-dawn light. On his fourth morning, he enters an old ruin and finds two big eyes staring back at him. It is a white, ape-like creature. The animal flees, stumbling through the daylight. He tries to track it, but it seems to have disappeared down one of the nearby wells.
He deduces from this new creature's appearance and behaviour that it lives underground, and he begins to understand the wells as being a huge ventilation system for an underground race. He imagines that the underground creatures are the labourers of the future society, and that they are only allowed to come out at night. He thinks of how in his own time there is a growing gap between the idle rich and labourers, and how the wealthy own huge estates where others are not allowed. He imagines that the overworld creatures have forced the underground creatures to work for them and have denied them access to the sunshine of the surface.
He soon learns from the peaceful surface creatures that these underground creatures are called "Morlocks" and that the surface creatures themselves are called "Eloi." When he tries to ask Weena more questions about the Morlocks, however, she becomes very upset.
I think it's important to realize that when the time traveller leaves in the end, he has with him a bag and a camera, so the reader can infer that he will return with proof.