I think it's about how when you have a really close friend so close that you two start to share a soul, and do things around each other you would never do around someone else (those nifty hand jive sequences for example) and then suddenly you two either grow apart, or they disappear.
Like a classmate who mysteriously transfers far away. And that happens to everyone (either you are the one left behind, or you are the one who leaves) before they grow up, right?
I see the Girl Who Leaped Through Time connection too (Megabusters!). I like the little white on black line animation with the sparkles at the end.
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