So it's been about 1 week, and having had some time to digest it I think I understand what's going on.
In chronological order, Reimu dies. Marisa is devastated, and asks Yukari why. Yukari gives a cryptic answer about the previous shrine maidens, and that Reimu's duty has ended. It seems what happened is that when their duties end, the Hakurei shrine maidens get sent to the outside world, as seen in the last page. So in order to say goodbye to Reimu, Marisa asks Yukari to be able to go to the outside world. This is when the school pages with Reimu and Marisa happen. However, they still have to say goodbye in the end, which is when the sea part happens. Marisa gets sent back, and on the beach by herself Reimu is found by the members of the sealing club.
Writing this down makes more sense, and if anyone has other interpretations of stuff I'd like to see your take on it.
inb4 the three of them find a way into Gensokyo, inadvertently cause an incident, and Reimu's really miffed because given that her duty as a shrine maiden has ended she can't do much about it. Or maybe she's not allowed in anymore.
