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Kingdom Hearts II
Right before the invasion of Hollow Bastion, Cloud warns Sora and company about Sephiroth, and his ways of the darkness. Later, as Sora exits the castle to go help defend against the invasion, Sephiroth appears. He asks about Cloud's whereabouts, but Sora does not answer, though he and his friends reveal that Cloud realizes that Sephiroth is the manifestation of Cloud's darkness. Seeing that Cloud is becoming enlightened and desires to fight him, Sephiroth takes his leave.
During the battle, Cloud is surrounded by Heartless, but Sephiroth intervenes, defeating them all in one swipe. Cloud intends to defeat his nemesis to escape the darkness, but Sephiroth only replies that Cloud will never be able to do so, and will always cower in the light. Cloud vehemently denies his dark half's claims, but Sephiroth is undeterred, and leaves just as Tifa arrives.
After the Master Control Program is defeated, Sora encounters Sephiroth at the Dark Depths. The villain again asks about Cloud, but Sora and his companions do not reveal anything. He then inquires about Sora, Donald, and Goofy's identities, but again, they refuse to answer. Sephiroth then notices Sora's Keyblade, and attacks, intending to test Sora's power and that of the Keyblade. Sora appears to overcome him, but Sephiroth just shrugs off the battle. Sephiroth complements Sora on his skill with the Keyblade but says that Cloud is the only one that can "eliminate him". Sephiroth then tells Sora to find Cloud so that they can settle their feud.
Cloud arrives later, and a battle begins, with Sephiroth desiring to draw Cloud into the darkness. However, Tifa protects Cloud, saying that Cloud does have light in him, and that, even if he does not, then he just needs to be surrounded by light. Nevertheless, Sephiroth and Cloud start off for another battle, and after Tifa's intervention, Cloud glows in light, surprising Sephiroth and letting his guard down. The two disappear in a brilliant flash of light.
Two years after the fall of Organization XIII, an injured Sephiroth returns to Radiant Garden after defeating and absorbing Cloud and holding his tsurugi. This implies that their battle lasted two years. He then went to what used to be Ansem's study, and is now his base of operations. He places his masamune in a glass case along with Cloud's tsurugi and walks to a desk. He stands there, and looks at a document revealing that at an unknown time, Cloud became a Heartless, Sephiroth, and after a bit met his Nobody and fused back with it, becoming whole; but somehow part of Sephiroth stayed separate. Sephiroth then changes his appearance to be a mix of his and Cloud's. He also grows seven more wings for a total of eight, proving that he has absorbed Cloud and become whole.
Upon leaving Radiant Garden, he encounters Madara Uchiha, leader of Akatsuki, an organization of mercenaries. Sephiroth draws his sword and attacks him after a short conversation. He is easily defeated by Madara and then Genesis appears and greets him as friend. They convince him to join Akatsuki.