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Apparently I missed this little puzzle.  Four statues in the Rest Area, one points to the sky, another points to East, the one points to the South, the last one does not point anywhere--her hands and clapped together in front of her chest.  East (right side), South (down), and sky (up) is the axis of a three-dimensional graph.  The fourth statue represents time, the element of the 4th dimension. Since it cannot be shown in a three-dimensional way, thus the last statue doesn't point to anywhere.

People might notice in Coco's Path, Hokuto discovers two drawings and one name list.  For those who took notes on details, Coco carved the stick figure onto the statue pointing south in Tsugumi's Scenario; but in Sora's scenario, she drew on the statue that points to sky.  In the Kid's perspective, the phantom Coco carved the drawing onto the statue pointing east.  As for translation of the official setting.  'Tsugumi' has a meaning of 鸠, a bird name in Japanese (Though it is actually written "月海", they have the same pronunciation).  In the Oriental legend, the divine beast guards the South is 朱雀(Suzuki), also a bird.  Sora's name means "sky", thus the statue pointed at the sky.  In both You and Sara's Scenarios, the drawing appeared on the east-pointing statue, which signified "two axis" = two endings...  Finally In Coco's path, the statue with her eyes closed and hands in front of her chest had the name list, hinting Coco was sleeping in IBF.

Now...  Something that is totally lost through translation!  You'aki's password she had from You'haru.  Of course it was planted.  "海月の虚空に秋涼し時鳥" is the original Japanese text for the password.  "海月" means "Sea and moon", which is the meaning of "Tsugumi", "虚" means illusive, here most likely signifies Blick Winkel.  "空" is Sora's given name in Japanese.  "秋" means autumn, here is a part of You'aki's name, "aki" = autumn = "秋".  "涼" is the first character of "Ryogo" ("Ryogo" in Japanese = "涼権"), "時" and "鳥" are most likely to be hints to Blick Winkel, "時" means time.  Blick Winkel travels through time and change history.  "鳥" means bird.  A bird flying in sky oversees the land animals, like how BW the 4th dimension being observes the 3D world.  The reason for creating this puzzle probably is to remind BW that, "the truth is about perspective, use another angle to see" etc.

    How did LeMU get rebuilt?  After the 2017 implosion of LeMU, the deadly Tief Blau virus brought much deaths to the world.  Leiblich attempted to hide the origin of the scourge--IBF's existence from everyone.  But to disintegrate IBF might cause further transmission of the virus, Leiblich decide to wait until the virus in IBF die out on its own.  Rebuilding LeMU is a critical part of the plan to keep a close distance to the underwater IBF.  Furthermore, You'haru used her connection with the famous Dr. Morino Shigezo, the doctor who originally gave her a chance to "genetic immortality", approached some capitalists and corporations that held grudge against Leiblich, to pressure the pharmaceutical company to speedily rebuilt the theme park.  Leiblich wanted to seal off the truth about IBF and Tief Blau, You'haru progressed with the Third Eye summoning plan--both of them benefited from the recreation of LeMU.  (This rumored to be an official explanation from Remember 11)

    Jewel Chocolate allusion in Coco's path.  Tsugumi talks to Hokuto alone.  You buy Jewel chocolate, gives you extra rings to collect.  There are 34 rings (17 * 2...), but to get all rings you have to keep buying the chocolate.  Tsugumi says he's just here to collect rings.  This proves that she's figured out the reason why 2034's incident is the replica of 2017, she acts along with it.  She also mentions she is only collecting the rings.  Originally, chocolate is the cause that one buys it, but the rings, as supposedly an "effect" of buying chocolate (ring = something extra, you want the chocolate), becomes the cause of buying the chocolate (you want the rings, chocolate = something extra), an equivalent paradox is the theme of Ever 17.  Tsugumi's here to gather the "effect" (searching her lost children), but in turn, she is also facilitating the rescue of Takeshi and Coco (becomes an cause).  So she's the "ring collector" is both a cause and an effect.

    2017 Sora and 2034 Sora.  Are they the same?  Nothing concrete is presented.  Though in Coco's and Sora's path, Sora mentions "W" and "Y" of split/clone people.  Not only alluding to the parallel universes theory, she is talking about her own.  Both Soras from the two time period share the same history, the experience before the accident.  They are different when 2017 Sora leaves LeMU and gains a physical body.  I (romantically) hope that two Soras would merge, in the end, of their memories.  I mean there's nothing saying that the 2034 Sora is not the old Sora who knew every detail of 2017 incident playing along with Kaburaki...

    2017 Takeshi woke up on ocean's floor... Sci-fi?  By that time Cure has already affecting Takeshi's body, thus making him seems revived.  It is unlikely that Tsugumi's vaccine caused his awaken, so there must be another time he caught the Cure virus.  Previously two situations when 1) Tsugumi was hurt in the Warehouse and lost a lot of blood and 2) They had sex in the Qualle.  I prefer the first theory because I doubt an engagement would spread cure... I mean it's just more likely Takeshi somehow got Tsugumi's blood in the first place and while they were leaving IBF Cure is working already.