Set in an alternate historical past based around World War I, Alek must team up with a crew of British Darwinists in order to escape German forces that want to kill him because he is a contender for the Austro-Hungarian throne. The world is on the brink of war and Alek, who is the son of an Austrian archduke, hopes to one day inherit his father's duties. At the moment, Alek's parents are away surveying military maneuvers in Sarajevo. One night, Alek is awakened by his master of ‘Mechaniks', Otto Klopp, and his fencing master, Count Volger. He is told that they are to do some midnight training on a "Walker" – a large metal clockwork war machine that walks on two legs and can be manned by a small team. Alek feels something is wrong as they don't usually practice so late and night and they don't usually make it a point to sneak out of the castle. Alek doesn't really like Count Volger as he feels like Volger doesn't give him the respect he deserves. He thinks it's because his mother is of common blood though she married into royalty. Because of his lack of pedigree, Alek may not be able to inherit the royal lands and titles from his father, a fact which makes him bitter. As Alek clumsily operates the Walker, he soon finds out that his father had ordered Otto and Count Volger to get him safely away to Prague in the event that something happens to him. Alek learns the tragic news that his parents have been killed in Sarajevo and that he is now considered a threat to the emperor's throne as he is next in line if the emperor dies. As they travel to safety, they are bombarded by attacks from German war machines and they have to go into hiding. Alek learns from Count Volger that the war between the Clankers (essentially the Germans and other machine-based societies) and the Darwinists (essentially the British and their genetically modified creature-based societies) has started.
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Meanwhile, Deryn Sharp, a young girl with dreams of following her father's footsteps as an air pilot, has dressed up like a boy and prepared herself to take the "middy's test", which is the test that will qualify her for the Air Service. Her brother, Jaspart, has already gotten into the Air Service and he's now helping Deryn achieve her dreams. The first order of the day is to get all the candidates used to the presence of the “fabrications” of natural philosophy or what they call the beasts used in the military and other industries. In England, where Deryn lives, almost everyone is a Darwinist and believes in the principle of cross-breeding to achieve creatures that have special abilities and functions. The candidates must learn how to handle a “Huxley” or a jellyfish-like creature that operates like a hot air balloon as it burns hydrogen gas in order to float into the sky. Deryn volunteers to go first and she is immediately comfortable high up in the air until a storm starts making the Huxley nervous. To save the Huxley from being impaled on a chimney or bursting into flames, Deryn and the fabrication are cut lose and they float away from the storm. They end up encountering a huge fabricated hydrogen breathing airship creature called the Leviathan. It looks like a flying whale with other species like birds and bats working in symbiosis with its form. The crew of the Leviathan help pull Deryn and the Huxley onto their ship. Deryn becomes an unofficial member of their crew as they don't have time to land the Leviathan due to an urgent call to France as a war is brewing on the border of Germany. On their way to France, Deryn learns the different battle drills, including how to feed the bats metal “flechettes” which allow them to drop dung bombs full of sharp metal that can rip apart the sails of an enemy ship.
Meanwhile, Alek, Otto and Count Volger have disguised themselves as locals in order to explore the small town of Lienz, pick up supplies for their journey and get parts to repair their damaged Walker. During their trip in the town, they inadvertently raise suspicions which causes the trip back to the Walker to be more dangerous than they expected. Count Volger gets injured and Alek kills a man for the first time. They manage to make it back to the Walker and get away with the goal of traveling to the Swiss border which is neutral in the war. Unfortunately, when they get to the border, German machines and soldiers are waiting for him. Though it is dangerous to operate the Walker at night, Alek sees no other option so they try to sneak past the Germans. Just at the last moment, the Germans notice them but Alek diverts their attention by putting one of their flares on his sword and throwing it far away from the Walker. This allows them time to get safely away. Alek learns that the Germans have been trying to instigate a war with the Darwinists for some time and they killed Alek's parents and made it look like the Serbians did it. Since the Serbians are allied with Russia, Russia will declare war on Austria, which is a Clanker nation. Then, to protect "Clanker honor", the Germans will declare war on Russia. Russia's ally, France, will then be involved in the war and eventually Britain will be dragged in, too. In essence, the German Clankers manipulated events to fulfill their agenda to engage in a war with the British Darwinists and Alek is at the very epicenter of the war.
Meanwhile, the Leviathan must make an important stop at the London Zoo to pick up Dr. Barlow, a renowned scientist of natural philosophy. Dr. Barlow has a pet “thylacine” called Tazza which looks like a fabricated creature that is a mix between a tiger and a dog. Dr. Barlow informs Deryn that she was the one who fabricated the species of whale that they're using for their airship. The scientist seems to think Deryn was assigned to show her around the ship so, even though Deryn would far rather do something else, she ends up being Dr. Barlow's personal assistant on board. One day, the Leviathan is attacked by German planes and, severely wounded, the Leviathan must make an emergency landing. They happen to land in the very place where Alek and his own crew are hiding. Count Volger tells Alek that the Darwinists are not their friends, but Alek, compelled by a sense of decency, insists that they have to help them as there is no food or fuel in the mountains where they crashed. Alek ventures out and finds Deryn, who's only slightly wounded from the crash. He planned on only dropping off some medical supplies and running off, however, before he can escape, some of the sniffer dogs from on board the Leviathan race towards them. Alek, afraid, tries to shoot them with his gun, but Deryn stops him. The captain of the Leviathan notices that Alek's gun is Austrian and they take Alek in for questioning since, as far as the Captain knows, Austrians are allied with Germans.
Back on the crashed Leviathan, Dr. Barlow asks Deryn to help her tend to some special eggs which she was carrying in the cargo. She refuses to explain what the eggs will hatch into, however she stresses that, for the sake of maintaining diplomatic relations with certain allies, these eggs are of utmost importance. Since Alek isn't exactly much of a threat, they allow him to roam the ship and he follows Deryn around. On a small scouting mission atop a Huxley, Deryn spots Alek's Walker and signals to her crew that an enemy is approaching. Deryn forces Count Volger to come down and talk to their Captain under the flag of truce. The two agree that Count Volger will give the crew of the Leviathan food in exchange for the release of Alek. As they are preparing to make the exchange, German airships appear. During the battle, the airships are successfully struck down, however Alek's Walker is severely damaged and can no longer properly walk. Alek asks Dr. Barlow whether he can and his crew can get a ride on the Leviathan to get to neutral ground. In exchange, he can supply the Leviathan with the Walker's engines which they can use to speed their way away. Dr. Barlow sees the importance of leaving their crash site as soon as possible since the Germans will soon be sending reinforcements. They manage to rig everything up just in time to get a head start in their escape from the German airships.
The story ends on a cliffhanger with Dr. Barlow revealing her plans to drop off the precious eggs in Constantinople, the center of the Ottoman Empire.
Best part of story, including ending:
I really enjoyed the creative descriptions of the Darwinist "fabrications". Scott Westerfeld satisfactorily explains the workings of the Leviathan whale creature, from the "cilia" appendages whose movements allow the whale to steer to how the bacteria in the whale's gut consumes the honey provided by a hive of bees and farts out the hydrogen that allows the whale to float.
Best scene in story:
My favorite scene was when Alek successfully attaches the Walker's engines to the Leviathan however the Leviathan can't get enough altitude because there is something weighing it down. They are forced to dump their treasure trove of gold bars out the window and onto the Swiss countryside in order to lessen their weight and allow the Leviathan to carry them away. It was a very humorous scene and made me wonder at what the locals would discover when the snow melts.
Opinion about the main character:
I like both the main characters of the story, Alek and Deryn. I like Alek because, even though he is royal and comes from a formal upbringing, he is still relatable as he feels ashamed when he messes up and is driven by a strong sense of decency to help even his enemies when they are in need. I like Deryn because of her fearlessness and I admire her drive to prove that she is capable of doing anything the boys can do. I wonder what will happen when Alek finds out Deryn is really a girl...