As one sentence, this is redundant. "At the end of the story they got married at the end." Break it into two sentences: "___ the end of the story they got married." "They got married ____ the end." From here, the first sentence needs "at" and a comma: At the end of the story, they got married. The second sentence, though, could take either "at" or "in". They got married in the end. They got married at the end. However, they have different meanings. The first, using "in", implies that the marriage happened after some sort of a negative event. Like, "She broke off the engagement three times, but they got married in the end." The second is just used to position the event on a timeline "at the end".

at the end