The series begins with a small circle of friends. There's Takayuki, the male lead, who's a bit of a slacker, and his buddy Shinji, a decent guy who gets good grades. There's also Mitsuki, an energetic girl on the swim team (who has an extremely faint but still budding crush on Takayuki), and her friend Haruka, a sweet but timid girl who has a huge crush on Takayuki. Mitsuki and Shinji help get Takayuki and Haruka together, and their relationship, while rocky at first, quickly flourishes. Haruka reveals to Takayuki her love for picture books, and that she has a dream of one day becoming a picture book author herself. She seeks a rare picture book called Mayauru's Gift, and, as a present, Takayuki finds it for her.
Takayuki is on his way to meet Haruka when he runs across Mitsuki, who shyly reminds him that it's her birthday. He takes a bit of time to buy her a ring for the occasion, which makes him late, allowing tragedy to strike. Takayuki arrives at the place he was supposed to meet Haruka, only to find a huge scene and yellow tape everywhere; Haruka has been hit by a car, and is now in a coma.
Fast forward three years later. Haruka is still in a coma, and everyone is in shambles (except for Shinji, who left for college during the timeskip, though he pops in and out of the story sometimes). Takayuki fell apart completely, blaming himself for the accident. Mitsuki nurses him back to prominence over the years, and in the process falls in love with him. The two form an uncertain relationship that is constantly clouded by guilt over Haruka.
Things only become even more complicated..when Haruka wakes up. She does not know that three years have passed; to her, the car accident might have been just the other day. The doctors make everyone promise to keep this fact a secret from her, as revealing it may be too much for her to handle. Thus the characters continue to live life, somewhat miserably.
Kimi ga Nozomu Eien isn't actually exceptionally unique in terms of plot material. It actually has a very standard feel to it. But it's the way the characters portray emotion that made this show so interesting--and yet so difficult-- to watch. Yes, middle parts of the series were actually difficult to watch for me, because it was gut wrenching watching these characters' suffer such emotional stress, and not seem to know any way how to help themselves. Amazingly, however, you actually come away from it feeling pretty good.