Although the ending of Yukikaze is basically EpilepticTree bait, [[http://www.imdb.com/title/tt0378730/board/thread/34698390?d=127396003&p=1#127396003 a user on IMDB]] weighs in and notes how careful observation throughout the OVA seems to indicate that it's not as confusing as it seems. The following post has been edited solely to fix grammatical mistakes as well as to fix the intended gender of Yukikaze (she is female, which is clearer in the novel).
It should go without saying that this will have spoilers for the entirety of the anime.
!Yukikaze Ending Analysis
"I've got a different take on the end of episode 5 - there are several contextual clues throughout the series which give us some pretty definite facts to lean on.
First is that Yukikaze is never deceived by the JAM. Yukikaze is consistently seeing through the JAM's deceptions which seem to fool every other human. But in every scene where the JAM are attempting to deceive the humans, Yukikaze is able to see through it. Because of this, I don't think the exodus was a mirage painted to fool the humans and/or Yukikaze - in such a case, Yukikaze would have seen it. I also don't think that the JAM are omnipotent or omniscient - they're not all-knowing nor infinite in any regard. Even if they are extraordinarily powerful, they still require time and energy to learn about humans. If, for some reason, the JAM had already known everything about the humans, including Yukikaze, by the end of the movie, then Ansel Rombert's final speech was actually contrary to the plot - that humans can buy time by confusing the equations of the JAM would have simply been a bald-faced lie. I can't imagine why the writers would intentionally mislead the audience that way. Perhaps the JAM knew everything about the humans, except Rei/Yukikaze, perhaps they simply hadn't acquired all the knowledge they wanted. From Rombert's speech, it seems to me that once the JAM learn everything, then the JAM's only intention left for mankind is annihilation. This is pure speculation, but it's possible the JAM have encountered other alien beings before visiting the humans - yet we see no keepsakes or any other remains of prior beings after all their knowledge is acquired.
Additionally, not only are the JAM unable to dupe Yukikaze, but she's able to dupe them. Since Yukikaze sees through the JAM's deceptions, I think it's safe to conclude that if Yukikaze believes she's deceiving the JAM, then they're being deceived. The amount that the JAM "know" about its subjects also seems to correlate with its ability to deceive them. (The) JAM know/knows a great deal about humans, deceiving just about everyone, but very, very little about Yukikaze, never being able to fool her.
So during the episode, the JAM were fooled by Yukikaze's operation. The humans had a fighting chance only because of that op; as soon as Ansel (and subsequently, the JAM) found out the entire mutiny and massacre were a ruse, they set off in hot pursuit for the escaping air force. When the JAM discover the massacre was just a setup, the mirage of the planet fades. What's key here is that the entire human air force ends up in that dark dimension where the JAM first tried to "take" Yukikaze. At the beginning of the episode, Yukikaze, Rei and Jack are about to be "taken" (and presumably, all other humans/machines were abducted and copied in this way) in that same dark dimension (complete with the flying particle clouds of tiny JAM fighters; look closely at the end of ep4/beginning of ep5). When Yukikaze threatens to destroy herself, the JAM give up and let them go. So it's possible that Fairy exists - and that the JAM merely abduct its victims into some kind of microcosm.
Even though the entire air force is about to be taken by the JAM, they've got a fighting chance & Yukikaze knows this, since she's the only one who knows how to fight the JAM. Things are pretty straight-forward from the time Yukikaze takes off from the Banshee to the end of the scene. Like I said, I don't consider that the JAM were anywhere near what could be considered all-powerful and so the humans have a fighting chance in the last battle.
Regardless of exactly what happened to Rei and Yukikaze, the humans make it back to Earth. The narration is assumed by Lynn - and unless the JAM had taken over Earth before mankind's counterattack through the portal, they probably could not duplicate her. And I highly, highly doubt that the JAM had already taken over all of Earth and fully learned about humans before the narrative starts - if that were the case, then the JAM would effectively be all-powerful (at least from a human perspective) and would have learned everything and probably destroyed humankind before Yukikaze was ever created. Also, if the JAM had totally taken over the Earth and set up some kind of Matrix-like existence for everyone, that'd be some pretty deceitful storytelling IMO. The idea that anyone in the story is subjected to a Matrix/Nexus/Solaris existence strikes me as paranoia.
While I can't be as certain about Yukikaze and Rei's fates, I think it's pretty simple. The white flash we see at the end of the battle scene was not just a transition to the next scene. There's an audible boom - this was the detonation of the Flip Knights. So I think that Yukikaze/Rei died. The debriefing at the end of the film could be nothing more than thoughtful recollections of past happy memories, or there could be some significance to Jack's opinion that Yukikaze and Rei are still alive and happy. If I have to decide, I think it's more likely that Yukikaze and Rei died on Fairy and chalk up Jack's final statement to wishful thinking and the final briefing scene to simple recollection on Jack's part. There are other times in the movie where characters are reminiscing (Lynn reflects on the time she first saw the JAM broadcast on TV during Christmas and that scene doesn't signify anything supernatural/metaphysical/etc). Additionally, because the Flip Knights detonate, I don't see how Yukikaze/Rei could continue living. I think it's more likely that not only did they die, but that the JAM itself was annihilated. I'm definitely curious about the significance of seeing Rei in the rear-view mirror and the debriefing at the end (assuming there is any). Maybe this carries a more obvious meaning exclusive to Japanese culture.
Final note about the JAM. I'm of the opinion that the JAM are not satisfied with its knowledge of mankind. If you look at how the JAM "learn" - it doesn't seem to really learn so much as it simply acquires data. The JAM are great at copying humans and their creations/inventions - but when you talk about creating and creativity- the JAM are limited. They/It has formed the mirage of Fairy and it designs aerial fighting machines (or maybe these were just acquired from a previous race), but outside of that, it demonstrates no further creativity. Even the makeup of Fairy could be chalked up to a total duplicate of Earth on a chemical/physical level - with green skies simply because it's illuminated by different stars. And their fighting machines could simply have been acquired from a previously conquered race. Also, the JAM seem to "think" more like a computer - as characters hint at logic and equations as part of JAM's thinking. But JAM runs into some problems when it witnesses human nature operating illogically; no amount of logic/equations can account for human irrationality. Ansel mentions this and his speech is pretty key to a lot of the intended conclusions IMO. So the JAM can copy, but not really create and they are severely confused by human illogic. Further evidence of this was heard earlier during a briefing in the series: we hear that whenever the humans invent a new technology, the JAM quickly duplicate it. It seems to me that the JAM are severely limited in certain areas of intellect which we take for granted. If that's true, this puts the humans on a more equal footing with the JAM.
So in the end, the JAM try to stop the humans, but it's not powerful enough and is ultimately defeated by Yukikaze/Rei, who sacrifice themselves to allow the humans to escape. While the heroes may have died, the ending is still a happy one, since the majority of the humans are able to escape safely."