Basically, there was an original timeline, the true timeline, where the MC and his harem became heroes, defeated the demon lord, lived the happy harem ending afterwards. However "glitches" occured in the "System" that manages the world.These "glitches" created alternate timelines where events played out differently from the OG. The story of this manga is one of the "Bad" timelines that was created as a result of the glitches. The fake hero who brainwashed the girls and NTR'd the MC in this timeline was never supposed to be summoned in the first place. In the bad timelines where the fake hero is summoned, and MC doesnt retake his position as the true hero, would always result in the absolute worst ending. The main heroine, Yunho, is actually the reincarnation of the Goddess. When she regains her powers, she fixes the timelines, deleting the bad timelines and fixing the rest to match the true OG.
The true timeline and ending depicts the true journey of the MC and his friends. Here, rather than the fake hero, the summoned hero is his sister, a little mischievious but kind girl named Shouko. The MC gains his true powers from the start, and fights alongside his friends/harem against the demon lord and its minions. The true timeline is basically a vanilla harem fantasy story, the MC fighting against evil and flirting with his harem. Eventually, it became less about fighting against evil, and more about quickly defeating the demon lord so he could marry his harem ASAP. The MC literally one shots a dragon by himself, because his fiancee Xiao said they could finally have sex after they beat that particular dragon. He then gets beat up by his harem for being a horny idiot. The MC then had passionate, vanilla snu snu times with Xiao for the rest of the journey.
Eventually, they confronted the demon lord, where the MC encounters Yunho, who's fixing the remaining glitches to ensure the happiest ending for the MC. The MC, momentarily regaining his memories about her from the other timelines, desperately wants her to be with him again, but she cant as further interactions from her could create more glitches. The MC goes on to defeat the demon lord and marries his harem. Besides his childhood friends, the summoned hero Shouko and the royal magician Narfe also join his harem and become his wives. A decade later, the MC is happily living with his harem, having fathered at least one child from almost each wife. As the MC thinks about his life thus far, he feels like something is missing, a hole in his heart. It is then Yunho appears before him, ready to join him at last.