Shadow Queen

"Then, you wretched fools... you will learn the error of your ways!"

- Shadow Queen

The Shadow Queen is the true main antagonist and final boss of Paper Mario: The Thousand-Year Door. 1,000 years before the game's events, she arrived in the Mushroom World with hopes of conquering it and making it her own. She was ultimately defeated and sealed away in the Palace of Shadow, where she remained for the last millennium and throughout the course of the game. After 1000 years have been passed, Beldam plans to revive her through manipulation of the X-Nauts. Mario and his friends enter the Palace of Shadow, her current location, to destroy her and save Peach, but in the end, Grodus provides Peach as a vessel for the Shadow Queen and she possesses her, forcing Mario and his friends to defeat the possessed Peach. Eventually after the Queen exits Peach's body due to being uncomfortable, she is destroyed by Mario and his partners for good.

Background
Legend tells that the Shadow Queen simply appears one day and wages war against the city where Rogueport now stands. She destroys the city and all who opposes her, forcing the remaining inhabitants to succumb to the queen's rule. She transforms a quarter of the city into the Palace of Shadows, which is where she resides in for the majority of the game's story. With the city under her control, the queen plans to conquer the rest of the world by creating an army of demonic beasts, including the three Shadow Sirens and the three dragons who end up becoming her pets.

Upon doing this, the queen creates the Crystal Stars, which hold the essence of the heavens and she plans to use to remake the planet how she sees fit. The Shadow Queen hides the stars in fortresses and castles across the land, and creates the Pit of 100 Trials to torture all who opposes her, also sending Bonetail to the Pit of 100 Trials to further punish anyone she chooses to send there.

When the queen is near the peak of her power, four heroes (a Toad, a Goomba, a Koopa Troopa and a Boo) emerge to stop her by stealing the Crystal Stars and using their power against the queen. They gather the stars, and mount an attack on the Palace of Shadow and the Shadow Queen. After fighting through the queen's entire army, she is attacked by the heroes and her body is destroyed, her spirit subsequently getting sealed in the foundations of the palace. Upon death, however, The queen curses the warriors, forcing them to prepare for the day when she would return.

Paper Mario: The Thousand Year Door
When Mario gathers all seven Crystal Stars, he releases the seal on The Palace of Shadow and chases Grodus through it. After defeating Bowser when he unexpectedly interrupts an encounter with Grodus, Mario once again finds him in the room where the Shadow Queen's spirit rests soon afterwards, who tells Mario and his friends that the queen needs Peach's body so that she can be fully revived. He summons the queen and presents Peach as a vessel for her, who the queen then possesses.

Once reborn, Grodus believes that he can now control the queen, the Shadow Queen almost eradicating him in disgust of his beliefs. The queen then notices Mario and his friends and offers them the position of her servants. They refuse, enraging the Shadow Queen and making her launch a devastating attack against them. Eventually, she becomes impervious to Mario and his friends' attacks, rendering them defenceless against the Shadow Queen.

Once the Crystal Stars travel to their home locations, allowing the people of each area to communicate with Mario, the Shadow Queen is distracted with their good wishes, allowing Peach to regain control of her body long enough to give Mario all her remaining power. Rejuvenated, Mario and his partners battle with the Shadow Queen further, and ultimately destroying her forever and releasing the relatively unharmed Peach, leaving Mario and his friends to celebrate.

Super Mario-Kun
The Shadow Queen also appears in the Super Mario-Kun manga adaptation of Paper Mario: The Thousand-Year Door's plot. As with most characters in the manga, she displays more of a comic side.

Powers and Abilities
The Shadow Queen is an immortal demon, having survived for a full 1,000 years while being sealed in the Palace of Shadow. She can also possess other persons, (as she did with Peach), and wields immense magical power, which she uses to create extremely powerful creatures and objects (as seen with the dragons and the Crystal Stars), as well as her own army of demonic beasts.

In battle, at her full power, she is immune to normal and defense-piercing attacks, and can only be made vulnerable with the power of the Crystal Stars. In her true form, she is able to use her hands to drain the health of her enemies and pierce their defenses. Her hands are also capable of smashing opponents to the ground, and are considered separate enemies; whenever they're defeated, the Shadow Queen can revive them the following turn. The Shadow Queen is also able to strike her opponents with lightning, an attack that is difficult to avoid due to its speed and defense-piercing nature. When in a dire situation, the Queen will often resort to attacks that induce poison, confusion, or allergies that prevent status changes.

One of the Shadow Queen's most deadly attacks is the use of several shadowy hands that come up from the ground and drag Mario and his partners down, or else stampede them for heavy defense-piercing damage. The Queen will also sic these hands on the audience members and drain their energy to restore her to full health and power. Her strongest attack is a series of black dark energy waves that hit Mario and his partner for heavy damage; however, this attack takes a turn to charge up, allowing Mario to avoid it with Vivian's Veil ability. The Shadow Queen also has the ability to temporarily raise her attack and defense by substantial amounts.

Personality
The Shadow Queen is a ruthless demon who cares only for herself and her aspirations, particularly subduing the entire world and remaking it over her image. She seems to rule her followers through fear rather than loyalty, as she uses her vast power to intimidate them.

Some of the Shadow Queen's speech and behavior vary somewhat between the Japanese and English versions of the game. In the Japanese version, she speaks in a considerably more down-to-earth manner. For example, when she sees Mario and his party members, she describes them as looking "agreeable", and when she offers them a second chance to serve her, she says if they agree she will "let bygones be bygones." In the English version, she speaks more formally, and is more condescending, backhandedly describing Mario and his party members as looking weak but possibly useful.

Trivia

 * The Shadow Queen is the only final boss in the Paper Mario series to not have any official artwork.
 * She cameos in Super Paper Mario as a doll in one of Francis Fort's rooms. The room is full of Paper Mario: The Thousand Year Door character dolls and posters.