All evidence thus far points to Nagisa slipping off her mortal coil by the end of Clannad~After Story~.
Which really pisses me off, because I think that the Clannad TV series would’ve worked MUCH better as a more straight-up rom com than the harem show that KyoAni shoehorned it into (see: awkward scene in episode 18 with all the girls trying to give Tomoya food, and which was completely inconsistent with the tone of the series thus far, in my opinion – it was KyoAni’s way to force the show into being a harem when it really wasn’t developing that way, as neither Fuuko nor Kotomi expressed romantic interest in Tomoya to that point, and Tomoyo really hadn’t either). Nagisa got screwed over! FAIL KyoAni, F-A-I-L!
And now they’re failing again by plotting to kill off poor Nagisa, and therefore screwing up Tomoya’s life royally… because, y’know, Tomoya didn’t have to deal with a ton of crap during his life as it is.
First off, I would cite the opening scene of the first episode of the After Story – here we see Tomoya and a child we can reasonably assume is his son riding a train together, and then going into a field of flowers like was seen in the first season’s OP. Where’s Nagisa? Nowhere to be found – and if you know anything about the game, this follows in with events late in the game where Nagisa has died, Tomoya is failing at life, but then he does end up reuniting with his son, Ushio.
But my assertion for that could be very easily waved aside, so I present to you the After Story OP:
If that doesn’t embed right, I’m going to bed mad. And in that case, you should click here.
Now, when you watch that, notice the different shots we get of Nagisa, Kyou, Kotomi, and Tomoyo. For the latter three, we all see shots in the background of older versions of them, most obvious in the case of Kyou as we see her in her job as a teacher. However, with Nagisa we only see shots of her as she is presently, which is to say, as a high school student. Hell, if you go later in the OP, we even see an adult Fuuko (she’s hugging a child I’m assuming is Ushio). So why no adult Nagisa?
Well, obviously, if she dies pretty young, you’re not really going to get to see her as an adult.
You might think I’m jumping to conclusions, but I’d point out that if the creators had wanted to, it would’ve been extremely simple to depict an adult Nagisa in the OP animation. Also, if the theme was to show all of the girls as adults, then why lave only Nagisa out?
There are other subtle hints in the OP as to there being a good chance that Nagisa wouldn’t survive the duration of the show. Kotomi is shown looking sadly at card with dangos on it which looks a lot like the dango drawings that Nagisa did for the Drama Club posters in the first season. Tomoyo stands alone in the snow looking downcast after a shot of her pinkie-swearing with someone (I’m pretty sure she did this in the first season with Nagisa toward the end). Fuuko hugging Nagisa and Tomoya’s kid is something I also interpret as not boding well for Nagisa, as Fuuko was, presumably, fated to die given the fact that one of the things talked about in the first season was that she wasn’t ever going to wake up from her coma.
Those are the things I can actually cite and back up with legitimate reasoning. What I can’t is that I get that feeling just from the way Nagisa appears in other shots during the opening, particularly at the end. I really don’t know how to explain it, but shots of characters smiling with their eyes closed with the background sort of blank behind them makes me feel like that character is dead or is going to be. The three shots of Nagisa right before we see Tomoya in a van also conveyed a sense of it being Tomoya remembering her from his school days, and his facial impression implies a sadness about that – these are bittersweet memories for him, and the only way they would be is if Nagisa is no longer of the world.
The final shot of Nagisa at the end of the OP also just makes me feel like she’s going to die. Putting a character into a setting that looks supernatural in a potentially spiritual way tends to cause that association in my mind. Nagisa disappears from view as orbs of light rise up around her. My money is on the poor girl dying.
There’s also the fact that the song has a somber feel to it – I wouldn’t say it is outright sad, but I do feel like it is a bit somber.
Anyway, this is just my interpretation of the OP; I really, really hope I’m wrong, honestly, because I love Nagisa. But I don’t have much hope for a happy end for Nagisa.