He got a concussion from the piece of concrete that fell on his head after saving his sister when the Tokyo Tower fell. It wasn't just a simple fever. He was feeling ill but kept it to himself for the most part, because he really wanted to get home, as Mirai mentioned later on in the final episode. Mari did notice a bump on his head, but didn't think much of it, again, because Yuuki wasn't complaining. Eventually, he started throwing up, and that was when it finally got worse. I'm guessing there was bleeding in his brain because it was all so sudden.
As for after his death and other characters seemingly acknowledging his presence. Actually, no one really "acknowledged" him. After the hospital, Mirai told me Mari, "I went to look for Yuuki since he wasn't there when I woke up this morning. He had me worried for a moment, but it looks like he's fine now," Mari had a look on her face. From then on out, Mari had changed. You could chalk it up to her being worried about her daughter, but it was obvious something's changed. It seemed like Mari saw that Mirai was not yet willing to let go of her brother, so she just left her alone.
There were also signs with Yuuki's backpack. Mirai was supposedly carrying it for him, but it really was just because no one else was there (Yuuki) to carry it. Even Mari offered to carry it for Mirai, not acknowledging Yuuki. Also, at the hospital, when Mari ran after Mirai after getting the note, she took Yuuki's backpack off the floor which "they" left...but in the scene earlier with the soldier whose ride Mirai was hitching on, Yuuki was by her side, carrying his backpack.
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