It tells the story of Karla and Kio, two fifteen-year-olds who have been stranded on a deserted floating castle called Nashido for ten years. Despite having no memory of how they arrived, the two survive as best they can, and even improve things (since both of them are low-key Gadgeteer Geniuses). The title character is an ornithopter the two are building to escape Nashido to the surface, which is at the center of a childhood promise Kio and Karla take very seriously: neither one of them leaves the other behind in the sky.
The tale kicks off with a bang when the relatively peaceful castle is attacked by a Dracolich of unknown origin and motivation. In fighting it off, Kio discovers that the rune magic which holds Nashido aloft is decaying, which might lead to them reaching the surface a bit faster than they meant to. Thereafter, the story follows Karla and Kio's quest preserve their home from dangers internal and external long enough to escape it.
The Clockwork Raven contains examples of:
- Acrophobic Bird: Averted by Karla after she transforms into a Raven in the Thunderhead arc. She quickly learns she has to think three-dimensionally to outsmart the dragon.
- After the End: Certainly after the end of something. Kio and Karla both have holes in their memories around when they arrived on Nashido—they call it "Year Zero" and refuse to speak of it while both privately trying to figure it out. All they know for sure is that here used to be people on the castle with them, and something wiped them all out. Then it turns out the same disaster may have also nuked the sky kingdoms.
- Breather Episode: The first arc, Visitor, features a prolonged fight in which Karla and Kio battle the monster that invades their home. The second, Wings, features less action and gives readers a chance to get used to the world of Castle Nashido. But there are still revelations—such as that dangerous letter Karla's been hiding.
- Break the Cutie: Kio is a pessimist, so he doesn't take things as hard, but Karla is easier to break—witness her complete devastation when she finds out Gunner was Dead All Along.
- Big Damn Heroes: Karla and Kio to each other, frequently.
- Catch a Falling Star: The serial loves this trope. In the very first arc, Kio gets snatched by the still-sentient arm of the destroyed dragon, and Karla rescues him using one of the fishing-line spearguns the two use to hunt birds. Two arcs later, Kio saves Karla from her abrupt transformation back into a human by piloting a broken-down ornithopter he jury-rigged to fly after realizing the ancestral tattoos on his face were actually runes with levitation magic. Yeah, it's that kind of story.
- Childhood Promise: An important plot point. The two leads have promised each other they won't escape the flying castle alone. When only Karla learns to fly, the promise is put to the test hard.
- Deus Est Machina: Discussed. Karla isn't comfortable with the idea that Nashido has a mind, since the castle has total control over her life.
- Dracolich: The bone dragon. Or potentially dragons. Nobody is quite sure whether there is more than one.
- Fantastic Caste System: The residents of the sky kingdoms believed themselves superior to the Rokhshan, who in turn treated the surface-dwellers as little more than livestock.
- Floating Continent: Nashido is a smaller example. The sky kingdoms play it straight.
- Geometric Magic: The ancient sky-dwellers used a rune-based magic system which Kio is only beginning to figure out.
- Heroic Lineage: Kio's got it, with statues and mosaics all over the castle praising the Rokhshan's heroic deeds. He thinks Karla shares that lineage, but the truth is a little more complicated.
- Homemade Inventions: Basically every piece of technology Karla and Kio use day-to-day. Highlights include pods that condense clouds into drinking water, spring-loaded retractable spear guns, and 'plumbing.'
- Homeworld Evacuation: Whatever disaster depopulated the sky kingdoms caught their citizens in the midst of one of these. Their aerial docks are crowded with the picked-over skeletons of people who didn't get out in time. Mara's letter also hints that the Harpooners were attempting something similar on the surface. Since Karla is the last Harpooneer, it can't have gone too well.
- Humanity's Wake: The characters' world. Averts Last of Their Kind because they know there are humans on the surface that survived the catastrophe. They just can't get down there.
- Indy Ploy: Favored by Karla when fighting bone dragons, piloting Raven, or doing pretty much anything. Kio would rather test things first, but can think on his feet—he just doesn't enjoy it the way Karla does.
- Infinite Supplies: Averted. The heroes only have what they can scavenge, and frequently have to dismantle parts of the castle to shore up things that are currently more important.
- Intrigued by Humanity: Played with. Karla and Kio are human, but they want to leave the sky behind and live the lives of surface people—people they are literally Higher Beings than.
- Magitek/Schizo Tech: An interesting combination of the two. Since the characters are restricted to what they can scavenge from passing islands and keep working at 20,000 feet, most of the technology is at a pre-medieval level—save for the Clock Punk flying machines, biologically-based oxygen and lighting systems, and the straight-up magic that keeps the castle flying.
- New Weird: Set amid the decaying ruins of a more traditional fantasy setting, featuring protagonists more focused on survival than any grand destiny, and mashing genres together like silly putty.
- Red Oni, Blue Oni: Kio is the blue to Karla's red.
- Wham Line: From arc 5 (Signal): "Who is Karla?"
- Wrench Wench: Karla. Kio sometimes qualifies (though not for the "wench" part), as the two can take over each others' roles when dire circumstances demand it.