The story picks off with the the Time Traveller just having woken up, the day right after arriving back in Richmond, 1891. He eventually makes up his mind to go back to 802,701 AD in order to save Weena from her unfortunate demise. However, this time around he notices things are drastically different. Earth's rotation on its axis is halted, and he notices that the sun has seemingly gone out.
Before he can arrive at 802,701 AD a mysterious creature to which the the Time Traveller refers to as the Watcher appears. This causes the Time Traveller to panic and stop the time machine. He falls out and finds himself in 657,208 AD. He eventually pieces together what happened. He realizes that a publishing of an account of his adventure by one of his friends caused humanity to take a different path, and advance on to become a type II civilization. This resulted in the creation of a new kind of Morlock. Instead of becoming the beastly herders of the Eloi, they're now a race of scholars, living on the surface of a Dyson Sphere.
One of these new Morlocks, Nebogipfel takes an interest in the Time Traveller, with the intention of convincing him to reveal the secrets of the Time Machine. After touring the sphere and looking at the advances of the new race of Morlocks, the Time Traveller decides to feign interest in cooperating, but instead use his time machine to go back to 1873 and stop himself from ever inventing time travel in the first place.
Things go from bad to worse as history starts to spiral out of control, and the Time Traveller can only watch as each timeline becomes more warped than the last.
It contains numerous references to the works of H. G. Wells.
This book provides examples of:
- Alternate Timeline: Some are shown, while others are simply implied.
- Ambiguous Ending: The story ends with the Time Traveller writing down the recounting of his adventures and sealing them in a Plattnerite packet, a time capsule, in the hope that it will travel in time to a faithful scribe. Before sealing the packet, the Time Traveller writes that he plans to go into the world of the Morlocks again, hopefully to return and add an appendix to the story. The book ends by saying that no appendix was found.
- Antiquated Linguistics: Despite being published in 1995, the book is written in the same Victorian style used by H. G. Wells in the original The Time Machine.
- Ascended to a Higher Plane of Existence: The Universal Constructors intend to bring Time Traveller and Nebogipfel with them to the beginning of time, but their bodies won't survive in the process, so they underwent a rather drastic modification.Nebogipfel, what am I? Am I still a man? You are still yourself, he said firmly. The only difference now is that the machinery which sustains you is not made up of bone and flesh, but of constructs within the Information Sea You have limbs, not of sinew and blood, but of Understanding.
- Author Filibuster: Downplayed compared to some of Baxter's other work as well as H.G. Wells' original novel, but the Time Traveller does have a few moments wherein he does this.
- Bad Future: The 1938 alternate timeline, relative to the Time Traveller's home of Richmond, 1891 is certainly this. World War I has been going on for 24 years and shows no sign of stopping, the common person now lives in a huge dome or an underground bunker, and time travel technology has allowed the war to be fought in the past. It's also implied that because of these circumstances, new generations of Englishmen born in said domes and bunkers are starting to bear a passing resemblance to Morlocks.
- Cephalothorax: A Watcher's body is a ball of flesh with dangling tentacles, a fleshy beak, no nostrils, and two huge human-like eyes.
- Deliberate Values Dissonance: The Time Traveller finds himself in various situations (and timelines) that clash with his own Victorian values and beliefs. Meeting female soldiers in the 1938 alternate timeline is just the tip of the iceberg.
- Determinator: The book starts with the Time Traveller off to go save Weena. He manages to see and survive an alternate World War I (which causes the death of his alternate past self), an atomic bomb going off in the Paleocene epoch, and the creation of a new universe. Despite all this, he manages to keep going and makes his way back to 802,701 AD and successfully saves Weena from her untimely death.
- Direct Line to the Author: The story itself is framed in-verse as a "lost manuscript" Stephen Baxter stumbled upon from a nondescript English attic in the reworked universe where the Time Traveller does succeed in saving Weena. It's also mentioned that the original book H.G. Wells wrote was a fictionalized account of the Time Traveller's experiences, as told to Wells by him.
- Domed Hometown: In the 1938 timeline, most British cities are domed with concrete as protection against the bombs of a prolonged World War I. The dome gets broken while we watch.
- Dyson Sphere: Nebogipfel and his fellow Morlocks live in one, which they use for their quest to gather all the knowledge they can. In another alternate history, the far more advanced Universal Constructors have apparently build a Dyson Sphere around almost every star in the galaxy.
- Earth That Was: In the First London timeline, human tampering with the Earth's environment renders the planet uninhabitable, and they depart for the stars.
- Embarrassing Middle Name: The Time Traveller calls his younger self by his middle name Moses, much to his chagrin.
- Fish out of Temporal Water: Nebogipfel and the Time Traveller are trapped without a time machine in the Paleocene and must survive. The Time Traveller realises how cooped up and "civilised" the 19th century has made him. He has worked in laboratories most of his adult life but is now forced to climb trees and hunt for survival.
- Forever War: The 1938 alternate timeline, with World War I still ongoing.
- Giving Radio to the Romans: In an attempt to alter the future, the Time Traveller gives the knowledge behind the Time Machine to his younger self he refers to as his own middle name, "Moses" who subsequently makes the technology public and setting the stage for a longer, bloodier and more twisted version of World War I.
- Godzilla Threshold: A prolonged World War I has prompted the British to increasingly recruit women into the military as well as give their remaining colonial subjects ever greater say in affairs.
- Going Native: At one point, stranded in Paleocene England, he gradually undergoes this. An encounter with a British expedition from the 1938 timeline, albeit later on in that timeline, stops him from going primal altogether.
Time Traveller: I'm going native!Nebogipfel: You are a native. This is England, remember?
- Also discussed by the protagonists:
- Historical Domain Character: The Austrian physicist Kurt Gödel appears as a supporting character during the middle part of the story. H. G. Wells (as "the Writer") is described as giving a lecture on a Babble Machine.
- Mind Screw: Just try and keep track of all the alternate timelines. The Reveal doesn't help at all.
- My Future Self and Me: The Time Traveller meets his past self after travelling back in time to the 1873 timeline, whom he calls by his middle name Moses. The story treats both versions as separate characters.
- Nanomachines: Universal Constructors are composed of nanomachines that also are made of smaller nanomachines. A Constructor can disassemble itself, move somewhere else and merge into one piece again. The smallest nanomachines can work at molecular, atomic and even subatomic level.
- Nice Job Breaking It, Hero!: His initial attempts to correct his own mistakes and save Weena end up backfiring spectacularly. As the knowledge behind the Time Machine winds up being made public by his younger self, eventually leading into a bloodier Forever War version of World War I. Which the Time Traveller himself winds up in around 1938.
- Properly Paranoid: The Time Traveller initially feels this way with Nebogipfel, given how he and his ilk resemble the "original" Morlocks despite being much more intelligent and amiable.
- The Reveal: The whole point of the adventure was the Time Traveller being guided across a Stable Time Loop by the Watchers, allowing the construction of the the Time Machine, the creation of the Constructors, and ultimately the complete reworking of the universe.
- Shout-Out: The Time Ships contains numerous references to other works of H.G. Wells such as "The Plattner Story", "The Land Ironclads", "The Chronic Argonauts", The World Set Free and so on. Nebogipfel takes his name from "The Chronic Argonauts"; the name of the carolinum bomb is taken from The World Set Free, among others.
- Tank Goodness: The large tank-like vehicle in the 1938 alternate timeline, capable of time travel, is called a land juggernaut, similar to the vehicles in Wells's short story "The Land Ironclads".
- Time Travel: Like the original novel, time travel is the central theme in the story.
- Trapped in the Past: The surviving members of a British time-travelling expedition from the 1938 timeline, albeit in 1944 find themselves trapped in the Paleocene thanks to an atomic bomb destroying their only means to return. They wind up setting up a small settlement called "First London" by the time the Time Traveller and Nebogipfel make their leave. Not only does First London thrive far beyond even the Time Traveller's expectations, but their distant descendants leave Earth altogether and made the creation of The Constructors possible.
- Voluntary Shapeshifting: Universal Constructors can take any form that is necessary for the environment they are in and create tools from their cilia.