Prologue: The Great War

The great war between the birds and the beasts happened approximately 65 million years after the extinction of the dinosaurs for dominance over the land and sky. The bats, however, seeing themselves as neither birds nor beasts, remained neutral throughout the conflict. Finally a compromise was reached; the birds would control the sky, while the beasts would claim the land. However, because the bats refused to take sides, they were banished from being allowed to fly during the day—not even allowed to so much as look at the sun—ever again; only emerging at night. The war is based on Aesop's Fables called "The Birds, the Beasts and the Bat."

Sun Freedom (Silverwing and Sunwing)

As Shade Silverwing looks at the sun, the owls destroy Tree Haven. While the Silverwing bats are migrating to Hibernaculum, he gets swept to sea. After Shade meets Marina Brightwing on an island, they head to the city. They encounter many other characters such as Zephyr, a bat who can see through the past and future, the cannibals Goth and Throbb, the rat kings Romulus and Remus, and humans who attempt to capture or kill them. Shade stays with Marina and finds his colony at Hibernaculum. After hibernating for two days, some members of the colony go on a journey to find Cassiel, who disappeared after finding the truth about the humans. When they find a building called "paradise" with bats living in it, the colony finds out that Cassiel is absent. While the other bats make themselves at home, Shade and Marina escape. After being separated, Shade ends up in the jungle, teams up with Orestes and finds out that sacrifices were being made at the Vampyrum Spectrum pyramid in order to banish the sun, and that Cassiel will also be a sacrifice. After Shade and Marina free the bats, owls and rats in order to defeat Goth, the owls permit the bats to look at the sun, while Marina and Shade become mates.

Underworld (Firewing)

Years later while Shade returns to Tree Haven for the first time, his son Griffin falls to the underground after accidentally dropping a fiery stick on his friend Luna. Finding out that dead bats live here forgetting that they died, he finds multiple bats with a strange glow. In the underworld, Cama Zotz orders the revived Goth to hunt down Griffin. After Frieda gives the sound map to Griffin, he and Luna attempt to escape from the underworld, and are helped by other dead bats that know each other. Goth kills Griffin, but Shade gives up his life for Griffin and Luna, who return to the upper world.

Silverwings

The Northern Bats have an Elder hierarchy, with one being elected high elder. Silverwings are based on the Silver-Haired Bat.

• Ariel: Shade's mother who raises Shade after Cassiel left. At the end of Sunwing, she is elected elder.
• Cassiel: Shade's father, who left the colony and see the sun. Shade notices his father is alive when Zephyr told him, finally Shade finds him in the abandoned Mayan temple being used by the Vampyrum Spectrum for sacrifices.
• Mercury: A male; the only one who stays with the females and their young outside of winter. He acts as a messenger amongst the Silverwings, befitting his namesake.
• Chinook: Shade's best friend. At the end of Sunwing he and Shade become friends and brothers because his parents died and he was adopted by Ariel and Cassiel at Shade's request (though Shade kept this a secret from Chinook, believing his once-rival would never let him hear the end of it). Chinook is frequently scared, like his step-nephew Griffin, but is brave when he needs to be, and he has good survival instincts. He was once very fond of dumping snow on Shade's head, though this may have just been an attempt to gain attention from Shade and Marina.
• Plato and Isis: Chinook's parents who travel with the other Silverwings to the human building at the beginning of Sunwing. They perished in the firestorm in the jungle.
• Jarod, Osric, Yara, Rasha and Penumbra: Newborns; friends and admirers of Chinook.
• Frieda: An elder of the Silverwing colony who is banded. She is the oldest bat in the colony, thus the wisest and helps Shade, even though he did something foolish. At the end of Sunwing, she dies at Bridge City. In the Underworld, she meets Griffin, telling him where to find the tree of life, a possible means of escape for him. She commends Griffin's desire to take Luna with him despite the fact that he knows she may slow him down.
• Bathsheba: A selfish elder of the colony, who scolds Shade for breaking the law and mistrusts the animals. In the television series, Bathsheba betrays them.
• Lucretia: One of the female elders who becomes a chief elder in Firewing.
• Aurora: One of the female elders.
• Icarus: A male; he is optimistic about what the bands foretell.
• Ishmael: A Silverwing captured by the Vampyrum for the ritual. He escaped, but his brother and others did not. While helping rescue Chinook and the other captives, Ishmael knocked his brother off of the Stone and was killed seconds later by Voxzaco on the sacrificial stone.

Vampyrum Spectrum

The Vampyrum Spectrum has a monarchy. They are carnivores and eat just about anything smaller than them, including other bats. They worship the Mayan bat god Cama Zotz. Vampyrum spectrum is the Latin name of the Spectral Bat.

• Throbb: Goth's fellow prisoner in the first book, who lacks courage and is forced to do his bidding. He is killed by a thunderstorm. His ghost serves Cama Zotz in the Underworld by aiding in an attempt to tunnel through to the world of the living.
• Voxzaco: A High Priest talking to Cama Zotz by eating strange, possibly hallucinogenic, herbs (shrooms). His spine is crooked due to age. He is able to interpret the stone calendar that serves religious purposes. He commits suicide by dropping a bomb that destroys the temple in an attempt to sacrifice 100 hearts to Zotz. In the third book, Zotz reveals that his ghost is suffering eternal torment in his stomach for his failure. While alive, he tried to remove the heart of Ishmael's brother, but Ishmael sacrificed his life for his brother, allowing Voxzaco to devour him.
• Phoenix: Zotz's female servant, whose name is derived from the phoenix, a legendary bird who rejuvenates itself through an immersion in fire. Phoenix fails to restore it with Goth, after Shade gives life for Griffin. She was to become Goth's mate when she was restored to life, but it is unknown when she will be able to do so, as it is not common for creatures to be sucked into the Underworld.
• Murk: A rare benevolent Vampyrum traveling to the Tree with Shade, Yorick, Nemo and Java.

Other bats

• Zephyr: An albino bat who lives in a church spire, a central hub for migrating bat colonies. He is very old and has lost his ability to see, but he uses his sonar with great accuracy. He also can see into the past and future using his ears. He has a vast knowledge of medicinal herbs.
• Scirocco: A long-eared bat that led a movement among the banded bats, saying they were promised to become humans. It is unknown what happened to him, or whether he was killed by Goth and Throbb.
• Penelope: A banded Brightwing who was originally part of Marina's colony. Like Marina, she was exiled from the colony for having a band. She later became one of those who followed Scirocco. She and her colony are devoured by Goth and Throbb.
• Caliban: A mastiff bat who leads a survival group living in Statue Haven. The group consisted of bats used by humans to carry fire (bombs) and were led by Shade's father until he was captured by the Vampyrum Spectrum. Statue Haven was based within the statue of Christ the Redeemer above Rio de Janeiro.

Dead bats in Zotz's kingdom

• Yorick: A 500-year-old Silverwing bat who always wants the way, because he has the map to the Tree. He lethally crashed into a tree, which severely damaged his wing and he has to suffer the pain.
• Nemo: A fish eater living in the coastal waters way down south. He has been dead for roughly 48 years. His death was caused by being eaten.
• Java: A foxwing with a wingspan of five feet, though she is a runt like Shade and even bigger than Goth. She becomes innocent toward any living thing. She does not have the gift of echolocation, which Shade does not like, but has excellent eyesight. She became lost after setting out for the Tree, having forgotten the verbal instructions the Pilgrims gave her, when Yorick found her way off course and invited her to travel with him. Unlike her two companions, she lived a full life and died of old age.

Other animals

• King Boreal: The king of the owls who appears only in Sunwing. When he goes to attack Bridge City, although he is persuaded otherwise by his son, Orestes. He is also persuaded to lift the flying ban on the bats, free the imprisoned bats at the various Hibernaculums and to also give the bats the freedom to fly in the daylight if they so choose.
• Brutus: An owl general who led the owls burning Tree Haven, after Shade glimpsed the sun. He dislikes bats and fought in the war to retrieve the Sun, although he wanted his species to keep control of the daylight skies and the owls won.
• Orestes: A young owl prince; son of King Boreal. One of those who persuaded the owls to lift their ban on the presence of bats in daylight. He was saved by Shade from humans. In the TV adaptation, he is Brutus's son.
• Romulus: King of the Northern rats who is considered a freak because of winglike flaps of skin between his fore and hind legs, which for his part led him to believe that bats and rats have a common ancestor. When his brother Prince Remus fled, he took command.
• Remus: Prince of the Northern rats. He is distrustful of everyone, to the point of paranoia. He scares himself into abdication from the throne, believing a plot to poison him was afoot.
• General Cortez: King of the southern rats, who appears only in Sunwing, where his youngest son is captured by Vampyrum. He and Shade stop Goth from resurrecting Zotz, and save Cassiel, Ariel, Chinook and Cortez's son. He also helps Marina save Shade. He is named after the conquistador Hernando Cortez who conquered the Aztec Empire.