Yukimaru and his friends investigate the Shiroyashiki as they look for their missing friends and run into the strange Room 303.

A floating ring has been passed down through Mikko's family for generations. Her grampa told her that the ring bears a promise of reuniting with lost ones who departed to the "other world." Mikko explores her world -- an endless network of tunnels -- in hopes of finding the "other world" one day... This is the side story to the film Inverted Patema.

When an unknown Arm Slave surfaces somewhere in the Taiwan Strait near mainland China, MITHRIL orders Melissa Mao and her team to go into a divided Hong Kong to investigate the perpetrator of the unknown Arm Slave. As the team continues to check into the reports of the unknown Arm Slave, the culprit is believed to be a potential SRT recruit back from Sousuke's training days in Belize when he was not recruited by MITHRIL.

From StarryHeaven:

The royal palace of the kingdom of Alba Forest received one letter of advance notice. That is, "We shall take the last treasure left behind by the late king to his beloved daughter, Violet." The sender of that letter was a group of robbers called the "Three Beasts." When Violet meets one of them by chance, the crow, her life changes greatly...!

In the southwest area of the Zemulia Continent, one will find the tiny Liberl Kingdom, a small monarchy that has managed to defy all odds against attempts to overcome them during war. Liberl is split into five regions: Rolent, Bose, Ruan, Zeiss, and Grancel. In the city of Rolent, Cassius Bright has raised two children by himself, Estelle and Joshua. He taught them everything they know himself, and encourages them to sign up to become apprentices in the Bracers Guild. Soon after, however, he receives a letter and has to leave on business, leaving Estelle and Joshua to fend for themselves. While working, they receive notice one day that their father's airship has gone missing. With this in mind, the two gear themselves up, and set off to find the ship and save their father. Of course, from there, nothing is at all like it seems. Few things are ever what they first seem to be in Zemulia, in fact.

"Do Your Best, Chrono-kun!" is a short manga that was included with the Japanese game guide. In full-color glory, this manga recreates the beginning of the game, where Chrono meets Marle during the Millenium Fair. The art style is a fair imitation of Akira Toriyama's, a plus for those who are so inclined.

In an future apocalyptic world the church once again has regained power, but not to do good, but to serve evil. Cloned priests, called "dragon fly" of the kirihito church use their power, however a shinigami has appeared to stop them and reclaim her past...

A collection of Dragon Kishidan oneshots and side stories:

One Day, Another Day
Set before the end of the series, it's basically a side story of a day in the Dragon Castle, kind of in Zoma's perspective.

Juuji ni Hikaru Hoshi
Takes place before the events of the actual series. This is a back story that shows how Lykouleon and Raselane met, introducing Lykouleon's uncle, Fieruto.

Mamono no Mori no Kioku
Another backstory that delves a little bit more into the relationship between Bierrez and Cesia before the series started. It also shows how Nadil became the demon lord.

Happiest Children
This actually has three little side stories in it. The first one is about Rune's dream about everyone dressed in drag, the second is about a little adventure that the three dragons go on, and then the third is like a day in the life of Alfeegi, Ri-ma, and Duma.

Crescendo
Backstory about how Lykouleon and Kaistern met and how Kaistern then became the Blue Dragon Officer.

CONFESSION - Thats
This is basically the backstory of Thatz and how he knew about Rath's little secret.

CONFESSION - Rath
Basically telling a lot about Rath, particularly his relationship with Kaister.

Based on Massively Multiplayer Online Game (MMOG). The beautiful Goddess Altea, creator of the tranquil worlds of Lagendia, plummeted into unconsciousness after being poisoned by her jealous, evil sister Vestinel. The poison can only be neutralized by an antidote made from the source of the poison itself - Vestinel's magic grail - which has disappeared into Lagendia along with sinister Vestinel herself. Able to communicate to her people only through dreams, the Goddess Altea calls upon the Heroes of Lagendia, via all-knowing prophets, to find the grail and save her from her eternal slumber. In their quest, the bold warriors must comb the lands for enchanged Power Stones, which allow them to speak with the prophets and unlock the will of Altea through her dreams. But the hunt for the Power Stones is not for the meek, as since the Goddess Altea's poisoning, the formerly peaceful lands of Lagendia have become home to throngs of deadly dragons bent on thwarting the grail's discovery and keeping the land in despair.

This story acts as a sequel to the original "Dragon Quest Monsters" game for the Gameboy. Kurio, a child who wishes to be a hero, is thrown to a world where monsters are found all over, and is asked to become their new Monster Master hero since the great tree is withering, the monsters are going berserk, and Terry, the previous monster master, has gone missing.

From DrMaster:
After his mother's death, Kuro Takagi transfers to Yotsuji Private High School where his father is the proprietor. But Yotsuji is no ordinary school. It holds a strange rule of “No students on campus after dark!” On his first day of attendance, Kuro and his classmates inadvertently break the school’s highest protocol and find themselves victims of a faculty zombie attack. Although they manage to narrowly escape, this is but a prelude to more encounters with the undead, especially after Kuro discover his own blood-ties and latent zombie abilities. From there, it's full steam ahead as this dark and intense action/comedy shifts into high gear.

Date Bashira is a series of stories about the Sengoku era in Japan. However, unlike most textbooks and historical mangas, Date Bashira does not focus on the Shogun or famous figures in history. Instead, it brings to light the untold stories of the things surrounding these famous figures. For example, one story tells about the role of how beautiful young men were always accompanying the shoguns into battle. As women were not allowed into a battle zone, the warlords would use these teenage boys to satisfy their sexual urges.

A different chapter tells the history of the wives of the Shoguns and focuses on the female role in the Sengoku era. As young women were forced into arranged marriages, usually as peace offerings or spies, their husbands usually die in battle at a very early age, as it was the era of war. Date Bashira discusses the idea of remarriage for these women and if they were really in love or were playing the role of a wife.

Date Bashira takes a different perspective at one of Japan’s most talked about era and even though it is informative, you never get the feeling of a lecture. The beautiful artwork, splash of comedy and the untold, yet interesting historical information really keeps the reader glued onto the pages. [vyc, mangahelpers]

A shape-shifter wolf who was once a human, but became a demi-immortal when his lover betrayed and murdered him, adopted an orphaned boy, who is now a young man. They travel together, exorcising evil spirits and demons. Trouble follows and finds them often, but they always manage to come out on the other side, pretty much intact.

From Viz:
It is the middle of the 21st century and Tokyo is expanding more and more, filling Tokyo Bay with landfill to make room for the bursting population. But suddenly Tokyo suffers one of its greatest earthquakes, and the landfill liquefies, creating untold damage in the newly-made urban area. The members of Self-Defense Force Rescue Squad Four are sent to help. But what they dig up is a plot of murder and destruction--one that wipes out nearly the entire squad and leaves its two surviving members, the fierce Rei and her cool, handsome partner Uozumi, in a fight for their lives.

There is only one place where they can find the work that keeps them alive, and the support so they can start uncovering the mystery that killed their squad: that's in the south-Shinjuku bar called Chicago. As the earthquake levels Japan's largest city and capital and leaves countless dead, rescue workers, Rei and Uozumi, search for survivors amidst the rubble of Bay District D only to find a mysterious string of dead bodies--bodies with bullet holes. Without warning, the pair is under fire from the air as a hail of gunfire rains down. Are these the killers, and if so, what is their purpose? Barely escaping with their lives, Rei and Uozumi discover that their squad is listed only as "collateral damage" and their records wiped clean.

J'on, a little Chinnkel free from being a slave from the higher races, has been given a mission to tell the people of Daar that if the world does not find peace, the world will be doomed. In order to end the war/unite the peace among the higher races, J'on sets out on a journey to find that answer and to see whether or not he is the chosen one that will free his people from them.. Note: This French comic contains little to some graphic nudity.

The Chrono Code, the key to a powerful weapon in the future, has been sent to 1994 and resides inside Ji Soo Jung. A gifted martial artist and the hope of her Kendo team in the upcoming national championships, Ji Soo Jung has no memory of her life prior to 4 years ago, and is searching for the lost brother she knows nothing about. She is catapulted into the middle of a violent struggle for the Chrono Code when different factions from the future start to fight over her, and she has no idea who is really a friend and who is really an enemy.

Once Demons and Humans were at war, and special warriors were needed to defend humans. Now a peace treaty exists between demons and humans. To uphold it human warriors now protect demons from other predatory demons. The Yosogi family is given this thankless task--and it's heir is young Akira, who can't even stand up against his older sister. But only Akira can sense the presence of demons, so he must become the next Demon Defender. But their grandfather has brought in a shy girl named Matsuri--and Akira is warned in a dream he must protect her at all costs!

From Dan of Population GO: Based off of The Song of the Nibelungs comes a manga about bravery, honor, and heroism. As the last of his people, Siegfried will stop at nothing until he becomes a legendary knight whose story will last eternity. If his legend lives on forever, then so will the memory of his people...and that is his sole reason for going on. 

It is the year 4088. It has been over one thousand years since the Crisis of Systems (Lost Property), which resulted in the destruction of four planetary systems, leaving only a single inhabitable planet, Zion. Mankind is forced to live in space colonies, since that one planet is constantly being invaded by alien life forms that have come to be known as Victim.

To stop the aliens and to allow people to land on Zion, mankind has developed the astronomical humanoid weapons, Ingrids, also known as Goddesses. G.O.A. (Goddess Operation Academy) is a school dedicated to the training of young men to pilot these Ingrids...

Set in 2194 AD, China, which is now a prosperous, super-modern country. The characters are mostly reincarnations of warriors from the 3 Kingdoms period. The story begins in Shin Yokohama with main chara Todoroki Ranshirou driving around & causing a ruckus with his bousouzoku called Yokohama Road Stars, when he gets a mysterious package from his father. Soon after he's attacked by Blades and makes an astonishing self-discovery... that he's the reincarnation of Sun Ce!