Rei's actions are indirectly trying to help Akane and her friends
Rei's actions are justified
The Alone (and maybe Rei) want to CONQUER EARTH!When Kenjirou first gives Akane the red key he mentions that the Manifestation Engine was a byproduct of creating the Vivid System (it is hinted that the Vivid System requires a lot of power). Kenjirou also predicted that Alone would eventually attack and he created the Vivid System as a means of defeating/defending against them. If this is all true (as all this information is mentioned within the first 2 eps) that means the Alone are attacking the Manifestation Engine in order to render the Vivid System useless and thereby remove the only threat to whatever their plan is (conquer earth maybe?). Rei may be either working for or with the Alone depending on how their separate (if they are at all) goals relate. And the incident seven years ago was a previous attack by either Rei or an Alone (conclusion drawn from the red ribbon like object seen floating above the Engine) in an attempt to prevent the Engine from being completed.
Energy upgradeThe Manifestation will be unable to fully support all four of the Vivid girls and the planet's energy usage. This will result in either:
It's all magicThe Manifestation Engine and the Vivid System are magitech, based on the kind of powers that Rei has (hence her being 0 in the Numerical Theme Naming). Rei wants to destroy the engine because it's using up too much mana, or something like that.
There is no magicRei's bow seems to be two large pairs of (most likely crow) wings that can shoot energy arrows. The feathers are actually a form of armor to protect whatever advanced tech may be inside the bow allowing it to re-energize the Alone. The Alone themselves are just advanced war machines drawing energy from their own Manifestation Engine.
Rei has 10 arrowsIn the second episode when she revives the Alone using her bow a flower appears on her scarf and one of the petals burns/fades away. A high enough quality image will show that there are 10 petals to begin with before the first one vanishes. This leads to the conclusion that she has the ability to revive 9 more Alone (excluding double reviving as that has not yet been shown possible).
The attacks on the manifestation engine are in self-defenseThe manifestation engine siphons energy from the parallel dimension which is the home of the Alone. The Alone need this energy to survive. When the humans keep stealing their energy, they will all die. Their only hope is to destroy the manifestation engine and prevent the humans from rebuilding it. So their attacks on the manifestation engine are merely self-defense.
The Alone want to fuse with the Manifestation EngineThey draw their power from the Engine (said so in episode 2) and plan on using the increased energy to avert some kind of tragedy that Rei (and who ever else is working with her) knows about.
Akane isn't a normal human, having been changed by the accident seven years ago.This is why she can go toe-to-toe with a kendo expert, or her Improbable Aiming Skills during the episode 2 flashback. It's also why she's the only one who can use the red ignition key. Whatever happened seven years ago led her to be Touched by Vorlons, or alternatively...
Akane died in the incident seven years ago and was revived or replaced by something which believes itself to be Akane.She does grow tomatoes...
Momo will become a Sixth RangerShe's focused on a lot, and appears in lots of promotional material. Too much so to be just a side character.
Akane will have a Super Mode that involves fusing with Aoi, Wakaba and Himawari at the same timeThis series has the spirit of a Magical Girl anime, and if there's something that is almost always obligatory in those shows, that is the Frilly Upgrade. Akane acts as the other three girls' upgrade by fusing with them, but what about Akane? The answer is clear: She will power up by having all of her three friends fuse with her at the same time, becoming a Vivid much more powerful than the mere sum of her parts in the process. The name of this Super Mode will be, of course, VividRed. A possible variation for this guess would be that, if Rei does a Heel-Face Turn, she will also be part of VividRed.
There will be a VividBlackRei will ultimately perform a Heel-Face Turn and be replaced by another villain, then Akane will give her a key and they will get a fusion sequence just like with the other girls.
Rei can fuse with an AloneShe already has a system in place to powerup an alone and it would not be much of a stretch for her to have her own transformation. Her transformation plus her bow would let her fuse with an Alone.
About the HoverbikeThe reason it's not mass-produced is because only Akane can ride it. And the reason why only Akane can ride it is because she's a human-sized Manifestation Engine, the core of her being changed after the accident in the flashback.
Rei is an alternate-universe Homura AkemiHer line "Home run"/"homuran" in Episode 4 practically confirms it. Possibly she's trying to protect the Vivid team, in order to fufill her role in this world as Madoka's prophet.
Rei's Alone-empowering arrows are fueled with her own life forceThe Episode 5 preview shows that the 'flower' on her chest are actually ten ethereal feathers nailed on her chest, on the area near her heart. Whenever she fires one of those arrows that makes the Alone power up, one of those feathers vanishes. My theory is that those feathers represent her life force, and should all of them vanish, Rei will die or something even worse will happen to her. At some point in the series, drama will ensue because they are about to vanish completely.
Fulling the contractAfter Rei finally helps an Alone reach the Manifestation Engine one of a few things might happen:
Rei is being manipulated by the Crow.Since she is so desperate to revive her parents, Rei is the perfect candidate to dupe into destroying the world for a chance to get her parents back. However, the Crow and the Alones have no intention of fulfilling their end of the deal, and are just using Rei since she is the only one who can empower the Alones. Rei also does not seem to be aware that it was the Alones that caused the meltdown of the first Manifestation Engine, making them indirectly responsible for the death of her parents.
Rei's arrows can empower the Vivids too.At some point, either accidentally or intentionally, Rei's arrow will hit Akane instead of the Alone. The result will be a temporary power to her boost and the creation of VividRed.
The crow was directly involved in the death of Rei's parents.She did it because she wanted to break Rei's heart in order to make her emotionally weak and gullible enough to accept working for her. When Rei fulfills her mission, she will have outlived her usefulness.
Rei is an Alone.Actually based on the "Akane = Nanomachine Colony" WMG above. Rei is ostensibly the 'support' Alone with the ability to put other Alone into 'overdrive' and increase their powers. However, in the accident several years ago, Rei was split from the main body of the Alone before it perished (leading to the Parental Abandonment memory and her limited empowering ability). The crow is actually either another fragment of her main body as a whole Alone or a representative of the other Alones, sent to urge Rei to continue her duties.
There is an Evangelion Plot in there somewhere.Alones can be seen as are equivalent to Neon Genesis Evangelion's Angels, and the Manifestation Engine either has something they want to initiate their agenda or a trapped Alone they wanted to fuse with/liberate. The crow is just playing with Rei.
The Alone are actually good.One of the conditions of Rei's contract with them is that she must attend school (she even lampshades on it). The reason she must attend school is because after destroying Akane's world the Alone will rebuild Rei's world AND Akane's world and connect them making traveling between them (and therefore making friends with each other) possible.
Another Alone Chrysalis like the one in Episode 8 will appear around the end.And this one will actually reach the end of its development before hatching. The resulting Alone will be even more powerful than the normal ones, but it will still not make a bit of difference because The Power of Friendship always saves the day.
The Crow has over stepped her role and will be punishedHaving just eaten Rei and started on her plan to destroy the world regardless of Akane and co. having passed the test an Alone (maybe the one that appeared 7 years ago?) will show up just as The Crow utterly defeats the vivid team and destroy The Crow.
Akane comes from the same alternate universe as Rei.This is more or less an updated followup to the "Akane isn't a normal human" WMGs above with The Reveal from EP 11 in mind.
Defeating the Crow is the REAL last part of the test.Two words: Unreliable Expositor.
The character seen at the end of The Stinger......is not Rei. It's her Alternate Universe counterpart (with a different name, which is why the authorities didn't know about her when they captured Rei). To keep with the Homura Expy theme, not!Rei will be shown to wear glasses. Season 2 will also have Akane's counterpart from Rei's universe. She's...bitter.
Akane is genuinely a magical girlDuring the accident at the Incarnate Engine, Akane fell into the incarnate energy and was changed. By the time of the series, her speed and strength and coordination are super-human. Her ability to throw newspapers into slots is one example. And there's no reason to believe that Akane has any formal training in Kendo, yet she was able to fight Wakaba to a draw. She was relying on her inhumanly-fast reaction time and her extraordinary coordination, and was making it up as she went. Finally, there's Vividred. Kenjiro didn't design Vividred, and he was just as surprised as anyone else when it appeared. Also, according to the Crow, Vividred was using an entirely new energy source, different from and superior to the one used by the Incarnation engine or the Crow herself. Akane took advantage of some of Kenjiro's technology in docking to create Vividred, but Rei had no key, and much of what happened transcended his technology. It can only be because Akane truly is a magical girl.