The race to obtain the lost Ainu gold is nearing its peak, as even more formidable ex-prisoners are set on keeping their tattooed skins intact. Saichi The Immortal Sugimoto and Asirpa can finally move forward together, but Asirpa's time with Kiroranke and Ogata Hyakunosuke has slightly altered her ambition and strengthened her determination. As their party leaves the Russian territory, they gain a peculiar follower. Meanwhile, Toshizou Hijikata's crew makes major moves to get invaluable skins, falling into the poisonous trap of a dangerous convict. Although each group possesses a strong advantage over the others, even First Lieutenant Tokushirou Tsurumi—the most powerful and ruthless contender—cannot advance without Asirpa's help. However, his ominous plans for when they will inevitably meet remain a mystery.

Jougorou Kobato has a habit of inserting himself into other people's problems. After realizing his detective skills are neither wanted nor appreciated, he makes an agreement with his shy friend Yuki Osanai to become ordinary together. Now entering high school, they aim to be perceived as regular people, yet Kobato cannot help but fall back into his deductive ways when faced with everyday mysteries. Unfortunately, mundane occurrences are not all the duo stumbles across. As they go through their school days trying to avoid drawing attention to themselves, Kobato and Osanai at times get caught up in incidents that put their plan of a peaceful, average life at risk.

After the termination of the incredibly popular virtual reality MMORPG The World, a new version of the game—The World R:2—is brought online. On his first day in the game, newcomer Haseo thinks he has made some friends to quest with. However, as if mocking his sentiments, they kill his character just for fun. Luckily, he is saved by a mysterious, one-armed player named Ovan who offers to show him around The World. Alongside Ovan and his cleric friend Shino, Haseo enjoys a wonderful first year in the game. But this peaceful life is shattered when Shino's character is killed by a familiar figure notoriously known as Tri-Edge, whose victims have all fallen into comas in the real world. In a fit of rage, Haseo vows to find the elusive Tri-Edge and kill him. Taking place during Haseo's first year in The World, .hack//Roots explores the friendships Haseo built in the game before Tri-Edge ripped them away.

Coco, a humble dressmaker's daughter, has always been fascinated by magic and the witches who cast it, despite the strict precautions they take to hide their methods from the public. However, when Coco takes advantage of a golden chance to spy on the skilled witch Qifrey, she realizes that her favorite picture book was a disguised magic book all along! In her excitement, she immediately starts testing out the various spells. When a spell causes a disaster in her home, Qifrey rescues her just in time and decides to train her, realizing that she is the first lead he has found that could help him track down the Brimmed Caps—a dangerous group of heretics who experiment with forbidden body-altering magic and spread magical artifacts among the commoners. But before Coco and Qifrey can confront the Brimmed Caps, she is going to have to improve her magical skills and learn to get along with Qifrey's other apprentices.