Inuyasha‘s older brother Sesshomaru and the partially revived Kikyo, whose own version of what happened years ago brings the events into question. When joined by Miroku, a perverted monk whose bloodline is cursed, Inuyasha and Kagome learn the truth: that the initial conflict between Inuyasha and Kikyo, revealed to originally be lovers, was caused by a devious half-demon named Naraku. The evolving Naraku is revealed to be born from the soul of an evil man named Onigumo inhabiting a body created by countless demons as part of a pact gone awry and who also placed the curse on Miroku’s family.
Naraku is after the Shikon Jewel shards for his own ends. Inuyasha’s group is soon joined after by Sango, a demon-slayer whose clan was killed when her younger brother Kohaku fell under Naraku’s control. Over time, Inuyasha enhances Tetsusaiga as he contends with Naraku’s minion incarnations like Kagura and the reanimated Band of Seven. Inuyasha’s team is allied by Sesshomaru, Kikyo (after learning that Naraku was the one who killed her), and a wolf demon named Koga who wants to avenge his comrades while flirting with Kagome.
While Naraku momentarily removed his heart in the form of the Infant, who later attempts to overthrow Naraku through his vessel Moryomaru, Kohaku regains his freewill and memories as he attempts to help out of guilt for indirectly killing his father. During that time, Seeshomaru settles things with Inuyasha to enable his brother to perfect Tetsusaiga to its optimal abilities. Eventually, after Koga is forced to stand on the sidelines while Kikyo posthumously used the last of her power to give Kohaku a second chance at life, Naraku finally reassembles the Shikon Jewel.
Although Inuyasha and his allies defeat him, realizing his true desire is for Kikyo’s love despite his hatred towards her and that it can never be granted, Naraku uses his wish to bring himself and Kagome into the Shikon Jewel. But Naraku’s wish is revealed to be the desire of Magatsuhi, an ancient demon who was sealed in the heart of the priestess Midoriko before it became the Shikon Jewel. Having aided Naraku in a temporary body prior to his defeat, Magatsuhi intended to have Kagome make a selfish wish so she and Naraku would be trapped in conflict while he can regain his physical form. But with Inuyasha by her side, Kagome wishes for the jewel to disappear, which destroys Magatsuhi while allowing Midoriko and Naraku to finally be at peace. The action, though, causes Kagome to return to her time with the Well sealed, causing her and Inuyasha to lose contact for three years.
In that time, the Sengoku period changes drastically: Sango and Miroku marry and have three children together; Kohaku resumes his journey to become a strong demon slayer with Kirara as his companion; Koga becomes leader of the wolf demons and marries Ayame; and Shippo attains the seventh rank as a fox demon. Back in the present, Kagome graduates from high school at the age of eighteen, before she finally manages to get the Bone-Eater’s Well in her backyard to work again. With approval from her mother, Kagome returns to the Sengoku period where she stays with Inuyasha and becomes his wife for the rest of her life.