The premise of the book is that Lewis Carroll's novel Alice in Wonderland was fiction, but that the character Alice is real, as, indeed, is the world of Wonderland. Carroll's novel is said to have been inspired by the images, ideas, and names related by Alice to the author, whom she had requested to make a book of her personal history. The theme of this book is loss of innocence.
The book's prologue tells of Reverend Charles Lutwidge Dodgson showing Alice Liddell (who claims her name to be spelled 'Alyss') the manuscript for Alice's Adventures Underground. Alyss is shocked by the book's contents and refuses to speak to Dodgson ever again.
The story then begins many years earlier, on Alyss' seventh birthday, in the Wonderland of Alyss' memory, which is ruled by imagination and is the source of all imagination for all other worlds. Wonderland features a class system similar to that seen in England during the 17th century, though on a far more minimalist scale. The government is a Queendom with an advising Parliament dominated by a playing card hierarchy, with the Heart family at the top of the proverbial stack (i.e. the Wonderland Queen is a member of the Heart family, and the parliament is composed of reigning members of the Spades, Clubs, and Diamonds). Females are the dominant sex in Wonderland, as the ruling families are matriarchies.
Wonderland, ruled by Queen Genevieve Heart, is still recovering from a bloody civil war between White Imagination and Black Imagination, which ended twelve years prior to the beginning of the story. Enough time has passed for those in the middle echelons of government to forget the day-to-day horrors of war and focus once more on the petty intrigues of a land at peace. Alyss' companions in her final hours in Wonderland include tutor Bibwit Harte (whose name is noted by Dodgson as being an anagram of "White Rabbit"), the Queen's bodyguard Hatter Madigan, Alyss' best friend Dodge Anders, childhood troublemaker Jack of Diamonds, and military commander General Doppelganger. During a bloody coup d'état led by Alyss' murderous Aunt Redd, the enemy of White Imagination, Alyss is forced to flee Wonderland in the company of Hatter Madigan, with Redd's top feline assassin (called only "The Cat") in pursuit. Queen Genevieve and Redd clash against one another in a final battle as Alyss barely manages to escape from the palace; Genevieve is killed by Redd. During this bloody battle, Dodge's father, Sir Justice Anders, is murdered by The Cat. The two fugitives, Hatter and Alyss, enter an inter-dimensional gateway called the Pool of Tears, from which they emerge into Earth through an exit portal: a puddle. Alyss is separated from Hatter during the journey and she arrives in London, England, and Hatter in Paris, France. Lost and alone, Alyss spends some time with street orphans, then finds herself adopted by the Liddell family, whereby she is given the name "Odd Alice" for her tales about Wonderland and the way she insists her name be spelled. When Dodgson plagiarizes her stories for his own imagination rather than write them verbatim, she shuns her imagination and resolves to believe Wonderland false and lost to her forever.
Meanwhile, Hatter is searching every corner of the world to find the lost princess. Believing that men dealing in headwear are men to be trusted above all others, he stops in every hat shop he can, inquiring the whereabouts of Princess Alyss Heart. Along his search he also trails people alight with the glow of White Imagination, knowing that Alyss would most likely glow the brightest. In the process, he becomes a mystery to people on Earth, who catch glimpses of him and create legends of a blade-wielding man on a strange quest leading him to headwear merchants around the world. After thirteen years of searching for the lost princess, Hatter finds Dodgson's book; he uses this to track down the author, and in turn, find Alyss, who is now twenty years of age. Upon arrival in Oxford, Hatter discovers that the princess is to marry to Prince Leopold. Before Hatter is able to rescue the princess, he is unexpectantly wounded and driven back to Wonderland. Dodge himself goes into the Pool of Tears, and rescues Alyss.
For thirteen long, hard years, the people of Wonderland have suffered under Redd's dictatorial reign of Black Imagination. The Wonderlanders still loyal to White Imagination have gathered within the Whispering Woods and have been surviving on their own, led by military leader General Doppelgänger and Bibwit Harte. Named after their long lost princess, they are called the "Alyssians" and stage battles and skirmishes against Redd's forces, attempting to weaken her grip on the throne with no avail. After thirteen years of no sign of Alyss ever returning home, morale within the camp is low and the Alyssians are considering turning themselves in to Redd.
However, Alyss returns to Wonderland and she is immediately taken in by the Alyssians, who rejoice with a wave of new hope and promise. Dodge Anders has become obsessed with avenging his father's death and becomes a bitter, nihilistic individual. With the assistance of the Alyssians, Alyss is able to find and locate the Looking Glass Maze, which is the manner by which all future Queens obtain their full strength and power necessary to rule Wonderland. When Alyss passes through the maze, she finds her intended Heart Scepter and moves on to fight against, and defeat, Redd. While Alyss and Redd battle, Dodge fights against The Cat; Dodge kills The Cat three times, leaving The Cat with one more life left; Hatter, Genevieve and Redd had all taken previous lives from The Cat's original number of nine. Redd, seeing her imminent failure against Alyss, throws herself into the Heart Crystal and is followed by The Cat.
- Alyss Heart (Alice Liddell): The Princess of Wonderland forced to flee to the real world when her Aunt Redd takes over Wonderland, slaughtering those who stand in her (Redd's) path. Alyss is eventually forced to adjust and adapt to the world around her. She shuns her imagination, finally to the point of believing Wonderland to be nothing but a dream.
Like the Alice of Lewis Carrol's books, Alyss is an exceptionally strong-willed, beautiful and (even after assuming the throne) free-thinking young woman. On multiple occasions she proves herself not only an exceptionally powerful adept but highly intelligent, like her mother and indeed her aunt. Like many protagonists, Alyss shares characteristics with her arch-enemy. Like Redd she does not enjoy the burdens of upholding the laws of White Imagination, love, justice and duty to the people and wants to be free to do as she pleases but unlike Redd she does care about all of those things and rules Wonderland selflessly. Alyss can be hard-edged and proud however and is a fierce opponent in combat, earning her the title of "Warrior-Queen" which was compulsory for all of her ancestors. Nevertheless she is a fair, kind and wise individual, earning her the respect and admiration of those around her.
- Hatter Madigan: Based loosely on The Hatter from Carroll's books, he is the Queen's bodyguard and the leading member of Wonderland's elite security force, The Millinery. During Redd's attack on the Palace, Hatter is given one last order by Queen Genevieve: to watch over Alyss until she is old enough to rule. Unfortunately, their escape from Redd's coup through the Pool of Tears goes awry and Hatter ends up in Paris (while Alyss emerges in England) with no clue as to the fate of the young girl he has been charged to protect. He spends the next thirteen years searching for her, his intent and promise to Queen Genevieve. He is an expert bladesmen, and his hat can flatten and split into S-shaped blades which is used like a boomerang fashion. After finding Alyss, he returns to Wonderland to help her in defeating Redd. Hatter Madigan has his own comic book series regarding his adventures searching for Alyss.
- Redd Heart: She is the main villain of the book and Alyss' aunt; based on both the Red Queen and the Queen of Hearts. As Genevieve's sister, she was raised and educated within Heart Palace. Being her tutor, Bibwit Harte has always viewed her fall into the diabolical as a failure in her education (and consequently his fault). The civil war fought within Wonderland was fought with Genevieve and Redd on opposing sides of the battle and ended with Redd's exile to the Chessboard Desert. She is a user of Black Imagination, a negative form of magic, and responsible for the murder of Alyss' parents. Since that time, Redd has crowned herself Queen and rules over Wonderland, promoting evil and Black Imagination. After a fierce battle with her niece, she jumps into the Heart Crystal, disappearing, leaving Alyss and the rest of her friends to wonder whether she is alive or dead.
Redd was the daughter of Queen Theodora and King Tyman of Wonderland. Whilst being highly intelligent and gifted with a powerful Imagination (in the Wonderland of the story, Imagination has magical powers), Redd was utterly unruly and arrogant as a teenager and exhibited behavior consistent with Oppositional defiant disorder. She was also addicted to artificial crystal, a drug common in Wonderland. Worried that Redd would make a tyrannical monarch, Theodora and Tyman removed her from succession and named Redd's sister, Genevieve, heir to the throne. Genevieve appears to be based on the White Queen. Being removed from succession took a heavy toll on the highly narcissistic Redd who already suffered from anger management issues and violent mood swings. In a fit of madness, she murdered her mother in her sleep before Theodora could announce her decision to the general public. Redd assumed the throne. However her sister, Genevieve, aware that Redd had killed their mother, defeated her sister and banished her to the Chessboard Desert. Redd is portrayed as an utter sociopath with sadistic and masochistic tendencies and like most clinically diagnosed sociopaths, she makes no attempt to mask her ruthless behavior, lashing out anyone when given the chance. What drives Redd toward enslaving Wonderland and its inhabitants is her megalomaniacal sense of entitlement. Exhibiting a classic Martyr complex, she appears obsessed with being removed from succession and is constantly consumed by feelings of anger and bitterness over it. Redd's pugnacious nature is evident in her self appointed style of address, "Her Imperial Viciousness." Redd is a practitioner of Black Imagination, the darker side of the Imaginative power spectrum which thrives on dark thoughts and emotions, similar to the Dark Side of the Force from Star Wars and the Dark Arts from Harry Potter. Users of Black Imagination are inherently corrupt and evil. If there's anything positive to be said about Redd it is that she is an astonishingly brave individual, displaying acts of fearlessness and an abnormal lack of nervousness on numerous occasions.
- Dodge Anders: Son of Sir Justice Anders, Captain of the palace guard, and a soldier in with her and with the rest of the Alyssians, with the purpose of killing The Cat, but he accidentally lets him escape. In the second and third books he is given the role of Queen Alyss' love interest.
- Bibwit Harte: The royal tutor to the Heart family, teaching them everything they have to know to be a good monarch. His name is an anagram of White Rabbit. After Alyss and Hatter disappear, he seems to work for Redd, but he secretly helps the Alyssians in their battle against Redd. When Alyss returns to Wonderland he decides to join the Alyssians openly.
- The Cat: Redd's assassin, loosely based on the Cheshire Cat from Carroll's original books. He kills Sir Justice Anders and attempts to pursue Alyss and Hatter when they escape from Wonderland. Unable to do so, he conceals this from Redd. He ordinarily resembles a muscular, bipedal feline equipped with melée weapons, but can take the form of a kitten as a sort of Trojan horse, and possesses nine lives. Over the course of the book, he loses all but one of these, variously to Hatter, Genevieve, Redd, or Dodge. At the last minute, he follows Redd into the Heart Crystal.
- General Doppelgänger: The commander of the Royal Army, made up of equal parts General Doppel and General Gänger. When split he is referred to as 'they', rather than 'he', and each is able to act independently of the other. General Doppelganger can also split into multiple Generals, of which each acts on his own free will. He is based on Tweedledee and Tweedledum.
- Homburg Molly: She is a "halfer" (half civilian and half Milliner) who helps Alyss and the rest of Alyssians to find the Looking Glass Maze, and eventually fights along their side in the battle of Mount Isolation. When Alyss is crowned as queen, Molly becomes her bodyguard.
- Jack of Diamonds: A pompous, cowardly, self-serving figure, the Jack of Diamonds is intended to become Alyss's fiancé when they are both still children. Following the coup, however, Jack takes advantage of the new order in Wonderland under Queen Redd. He plays both sides of the conflict, acting as a member of the Alyssians while at the same time delivering information to Redd about their activities. Jack often knows much more than he is telling, but decides not to reveal everything he knows, as that would ruin the lucrative business of playing a double agent. During the final battle with Queen Redd, his betrayals are discovered by Dodge, and he is subsequently taken prisoner by Alyss in the aftermath. He is most likely based on the Knave of Hearts.
- Prince Leopold: When he first meets Alice he kisses her hand and doesn't let go. After that he follows her around everywhere. Three months later he asks her to marry him. He loves the way she does things; she doesn't try to flirt with him, or amaze him, she is just simply herself, and still beautiful to him.
- Queen Genevieve Heart: Queen of Wonderland, mother of Alyss, and wife of King Nolan Heart. She is the ruler of Wonderland prior to Redd's coup. Killed by Redd on Alyss's seventh birthday. She appears to be based on the White Queen. She is acknowledged as a warrior queen.
- King Nolan Heart: King of Wonderland, father of Alyss, and husband of Queen Genevieve Heart. Killed by Redd on Alyss's seventh birthday. He appears to be based on the White King.
- King Arch: Ruler of Boarderland. Boarderland is a kingdom (a country ruled by a man) to which King Nolan is sent to attempt to gain as an ally against Redd. A deeply sexist and misogynistic individual, King Arch's views on women and Wonderland's status as a queendom (a nation ruled by a Queen) makes him reluctant to ally with Wonderland for fear it would have a negative influence on the female population of Boarderland.
- Sir Justice Anders: Captain of the Palace Guard and father of Dodge Anders. He is killed by The Cat on Alyss's seventh birthday. He is based loosely on the White Knight.
- Blue Caterpillar: Based on The Caterpillar from Alice's Adventures in Wonderland, Blue Caterpillar is the head of six oracle-like caterpillars (of which the remaining five are colored red, yellow, orange, green, and purple) who live in the Valley of Mushrooms and act as guardians to the sacred Heart Crystal. Never seen without his hookah pipe, Blue gives Queen Genevieve a warning of Redd's coup, and later tells Alyss how to find the Looking Glass Maze.
- The Liddells: Alyss's adopted family. Reverend (Dean of Christ Church) and Mrs. Liddell of Oxford and their three daughters: Edith, Lorina, and Rhoda. Also, notable in the household is the children's governess, Miss Prickett. None of the Liddels believe that Alyss tells the truth when referring to Wonderland.
- Reverend Charles Lutwidge Dodgson: The mathematics lecturer of Christ Church and author of Alice's Adventures Underground under the penname Lewis Carroll which, in The Looking Glass Wars, he wrote based upon Alyss's recounting of her life in Wonderland.
- Walrus-Butler: He is Queen Genevieve's butler; after her death, he becomes Queen Redd's butler. He is based on the Walrus from Through the Looking-Glass. He is extremely cowardly because he fears Redd and her power. After Redd's defeat and the ending of the battle he helps Alyss, Dodge and the others by taking care of their wounds.