Ship in a Bottle
Ship in a Bottle is a story written by Hyakunichisou 13. It ran in Issue 51 at http://s2b2.livejournal.com/291840.html, and is mirrored at http://www.shousetsubangbang.com/mirror/ship-in-a-bottle.
From fairyninjas.wordpress.com: "A cute and sweet tale of a young man who finds something unexpected, and another who ends up in a place he doesn’t understand."
From pinboard.in: "the one with the time-traveling plant alien trapped in a bottle"