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If you consider the case of just one blue-eyed person on the island, you can show that he obviously leaves the first night, because he knows he's the only one the Guru could be talking about. He looks around and sees no one else, and knows he should leave. So: [THEOREM 1] If there is one blue-eyed person, he leaves the first night.
If there are two blue-eyed people, they will each look at the other. They will each realize that "if I don't have blue eyes [HYPOTHESIS 1], then that guy is the only blue-eyed person. And if he's the only person, by THEOREM 1 he will leave tonight." They each wait and see, and when neither of them leave the first night, each realizes "My HYPOTHESIS 1 was incorrect. I must have blue eyes." And each leaves the second night.
So: [THEOREM 2]: If there are two blue-eyed people on the island, they will each leave the 2nd night.
If there are three blue-eyed people, each one will look at the other two and go through a process similar to the one above. Each considers the two possibilities -- "I have blue eyes" or "I don't have blue eyes." He will know that if he doesn't have blue eyes, there are only two blue-eyed people on the island -- the two he sees. So he can wait two nights, and if no one leaves, he knows he must have blue eyes -- THEOREM 2 says that if he didn't, the other guys would have left. When he sees that they didn't, he knows his eyes are blue. All three of them are doing this same process, so they all figure it out on day 3 and leave.
This induction can continue all the way up to THEOREM 99, which each person on the island in the problem will of course know immediately. Then they'll each wait 99 days, see that the rest of the group hasn't gone anywhere, and on the 100th night, they all leave.
Before you email me to argue or question: This solution is correct. My explanation may not be the clearest, and it's very difficult to wrap your head around (at least, it was for me), but the facts of it are accurate. I've talked the problem over with many logic/math professors, worked through it with students, and analyzed from a number of different angles. The answer is correct and proven, even if my explanations aren't as clear as they could be.
User lolbifrons on reddit posted an inductive proof.
If you're satisfied with this answer, here are a couple questions that may force you to further explore the structure of the puzzle: