Alexander can't believe that the Eloi are resigned to be taken and eaten alive by the evil Morlocks, so decides to do something about it and enter their lair to rescue his friend Mara (Samantha Mumba). He takes advice from the hologram librarian, and then travels to the scary skull-rock.
Inside he meets the Uber-Morlock (Jeremy Irons), who gives him a few answers, and tells him more about the history and the real world. Alexander is appalled that he has no respect for life, Uber-Morlock is angry back at him for challenging his actions.
The answer to 'the big one', Uber explains, is that the time machine was brought about by the death of his wife - so Alexander cannot use it to go back in time and change the past.
They get into a fight and Alexander punches the machine forward, taking Irons with him. His enemy falls outside the time machine's reach and ages rapidly, just like the Nazi in The Last Crusade. Alexander stops the machine many, many years in the future to see a landscape dominated by the bad guys - so decides to go back and save the day.
He returns to 800,000AD, sets the machine to implode and rescues Samantha Mumba. They get out the lair just as the machine erupts into a fiery blue ball of energy, killing all the bad guys in a huge, blue, death-ray.
Alexander then leads the Eloi people to further their civilisation, and starts with a new school taught by the hologram librarian.