Bear in mind that there is going to be spoilers for the entire game in this section. I know it's an obvious statement, due to it being an unanswered questions article, however I am putting it down in writing as a last warning to people who don't want to know about the plot.
Q: What is the Singularity?
A: I'm going to agree with a majority of the fans and say it's like a black hole. After all, if the Singularity "swallows everything and leaves nothing behind," to quote Pike himself, that sounds just like how the gravitational pull of a black hole sucks in nearby matter.
Q: Are Halley & Emmy the Plug for all Rare Majesties, or just the ones Pike had?
A: It certainly seems like CIMA are looking for one specific Plug, since nobody seems to indicate that they are looking for the Plug for the specific Rare Majesties. Plus, Ark mentions their resonances to Ivy in Jean's clinic at the end, even though Pike's Rare Majesties were destroyed. So CIMA probably would use Halley and Emmy for all of them.
A: Pike had two Rare Majesties, there were two kids he figured were the Plug. Halley was probably the Plug for the yellow one and Emmy was the Plug for the green one. Ark and the others didn't know exactly what the Plug was, so it's only natural that they assume Halley and Emmy are the Plug for everything. Also, when Pike talks about Jester's Purple Majesty, he mentions that Jester doesn't have the Plug. If the Plug is Halley and Emmy, then Jester did have them, he just didn't know they were the Plug and the wording "you don't know where it is" would make more sense; even though Pike didn't know which person was the Plug yet, he knew it was within your group. I doubt that Jester would realize the Plug was among them from wording like that, let alone the rookies who have no idea what it is.
Q: How come it took twenty years to find the Plug after the first opening of the Singularity, and it turned out to be two kids whose combined ages didn't even equal twenty?
A: The Plug can only be someone within a certain age range. When that person gets too old, the Rare Majesties find someone else to resonate with them.
A: The former Plug (who either survived opening the Singularity 20 years ago, or inherited it from the person who died opening the Singularity) passed away, and the Rare Majesties chose a new person (or persons in this case) to resonate with them.
A: If we go with the theory that all Rare Majesties have different Plugs, perhaps something must be activated within them before they will synchronize with whomever their Plug is. CIMA could have been preparing so this opening of the Singularity didn't fail, thus Pike might have only prepared his Rare Majesties recently.
A: The Singularity can only be opened once every 20 years, so a Plug wouldn't appear until then. That's why Esswood mentions it's almost at the limit; the Gate Guardians have that information from their battles with CIMA and know they can open it soon.
Q: What is the Base? We know that the Plug opens the Singularity, so what does the Base do? And why isn't CIMA so concerned with finding it?
A: It stops the power of the Singularity. That's why the Gate Guardians are looking for it but the CIMA never mention it; if something goes wrong when they open the Singularity, the Gate Guardians would be more concerned about life than CIMA (seeing as Pike didn't care about his men dying, while the Gate Guardians are all about protecting others).
A: It allows greater control of the Singularity, rather than simply opening a Black Hole and hoping for the best. Whereas with only the Plug, the Singularity opens on the spot, the Base can allow control of it opening wherever the user wished. CIMA don't have to worry so much about this because they can easily send it through a Gate the second it opens, thus the Base doesn't concern them.
Q: What are the Purple and Light Majesties, and why was Pike scared of Purple?
A: They are Rare Majesties, like the ones Pike had. Humans somehow acquired them, and are looking into using them to open the Singularity. Pike was afraid that Jester could open the Singularity and so he was nervous until he realized Jester didn't have the Plug.
A: Artificial Majesties created by humans to mimic the power of the Rare Majesties held by CIMA. Either Pike or CIMA as a whole found out about the experiment, so Pike was afraid it was fully tested and could open the Singularity in his dungeon.
Q: Why are CIMA going to open the Singularity when it would kill their food source?
A: CIMA and humans are at war, and they'd rather lose that food source than be overwhelmed by the humans' superior numbers. Considering Ivy lives among humans, she probably can survive on things other than hope; Pike did say it was only something low CIMA would desire.
A: They want vengeance for some past wrong or perceived wrong that was committed by humans against CIMA. What could be better revenge than complete annihilation?
A: CIMA wish to rule both worlds, and humans are in the way.
A: Maybe the earth as it stands now cannot support CIMA for some reason (Ivy might be an exception because of other factors that we don't know yet, or one CIMA living on Earth doesn't make a difference). The Singularity's power will make that null and void.
Q: Furthermore, why would humans want to open the Singularity if it's going to be used on them?
A: They are going to make sure to open it in the CIMA world, so everything there is sucked up instead. Either through manipulation of the Base (if indeed that's what it's used for) or by creating some sort of trap to allow the Plug and their Rare Majesties to go there.
A: They believe they can control it, possibly because it didn't kill everyone the last time. Now, whether they would be able to command it under their own power (or with a combination of the Plug and Base) is a different story altogether...
Q: Why did the Singularity open 20 years ago without destroying everything?
A: If the Base indeed does stop the Singularity's power or close it up, it could have been used before things got too bad.
A: Perhaps Falcken mentioning a Plug that didn't work out in relation to Doug's anger didn't mean a failure to open the Singularity. Maybe Elizabeth was the Plug 20 years ago, however the Singularity's opening was all wrong because her emotions weren't resonating in the correct manner. The Singularity opened, failed to destroy everything but gave valuable information to the Gate Guardians to start their own quest for the Singularity. Elizabeth most likely died either from the effort to open the Singularity or Falcken's rage over the failure.
Q: What is the transformation mentioned by Jester in the opening cutscene?
A: Transformation of the world following the Singularity's opening.
A: The transformation of someone into the Plug (and possibly the Base) needed to open and control the Singularity.
A: The transformation of conditions needed to open the Singularity in the first place.
Q: Are the builders and the various monsters really the same race?
A: They are, it's just the builders are either born with greater powers that allow them to take both human and monster form, or they are altered later on in order to create more builders. All the forms taken by CIMA are dependent on power.
A: The monster CIMA are genetic creations used to hunt humans, made either by the Majesty factories in the nests or by the builders themselves, and the builders are the real members of the CIMA race.
Q: How are CIMA born?
A: CIMA are born from Majesties, the amount of Majesties used determines the creature's characteristics. It probably takes a lot of Majesties or extremely large and powerful ones, to create a builder, and possibly multiple CIMA need to resonate together to minimize the strain on their bodies. Either Ivy's age is an assumed one (though she might be kicking herself for not making herself be older so Ark couldn't use that as a means of being in charge) or she really was created seventeen years ago (as a baby or a teenage figure makes no difference).
A: While monster CIMA are born en mass from majesty factories embedded within the CIMA nests, and bosses are created when builders resonate with Majesties, builders are born like normal humans. After all, Ivy has an actual age listed in the manual, and she and Ark specifically talk about their age difference in the beginning. Though considering how CIMA society is, I doubt there is more marrying for power and alliances than marrying for romantic reasons.
Q: At the end of the game, Pike mentions CIMA returning to Earth. What was that about?
A: CIMA builders used to be normal humans living on Earth. They were persecuted for whatever powers they had back then/a religion they practiced, and somehow ended up in the Gate World when they were trying to escape their pursuers. Whether it was the air in the Gate World or energy from the Majesties, their bodies began to evolve into the way we see them in the game.
A: CIMA existed as we know them from the game, however they lived in the human world. Long ago, they were preying on humans and it led to a war. Due to greater numbers, humans overwhelmed CIMA and they were forced to retreat to the Gate World (either they created the dimension themselves or it was their home dimension before migrating to the human world).
A: The game's world in medieval times was a sword and sorcery world much like any fantasy RPG. CIMA as we know it are descended of some group (evil, predatory or persecuted) who were banished by sorcerers who believed they were doing what was best for the human race.
Q: What is the Prophesied Time that Ivy mentioned before she transformed?
A: The time when CIMA will finally return to earth. Of course, considering their conflict with humans, to accomplish this they have to destroy humanity first.
A: A time when they will get revenge on humanity by destroying them (if some conflict between the races did indeed happen long ago).
A: The time when the Singularity will open and devour all it comes in contact with.
Q: Why is Pike acting alone when there are eight other CIMA as powerful as him?
A: They are each working on their own because they can cover more ground that way. Pike is either too proud to ask for their help once he locates the Singularity, or he is too confident in his abilities to think he will need it (after all, Ark couldn't even scratch him till Ivy did her deus ex machina transformation and even then he still thought it wouldn't work).
A: Each member of the Crimson Nine wants the glory of opening the Singularity for themselves. So they aren't going to be contacting any other members if they find something...in fear of having their prey stolen out from under their noses.
Q: Why is Ivy helping humans if she is a CIMA?
A: As a child, Ivy was rescued by humans who'd mistaken her for a normal girl. With the help of her kind foster parents, her ideals were shaped to be closer to what regular humans believe in. Whatever scant knowledge she has of CIMA is memory from her childhood, and her transformation abilities are instinctual rather than learned, but she is as in the dark about a lot of things as Ark and the others (thus why she knows about a legend like the "Prophesied Time" and not about things like the Plug and Base).
A: Ivy was saved by humans for whatever reason, and came to realize something about the relations between their races as a result. Thus, she decided to leave the Gate World and reside among the humans.
A: There exists a division of CIMA who oppose the Crimson Nine's plans and wish to create peace with humans. Ivy is an agent they sent to infiltrate the Gate Guardians and help protect people from the plans of the other CIMA.
A: She was originally sent to the human world as a spy, but came to love something about humanity and never returned to the Gate World.
Q: Why did Ivy wait so long to transform into a sword? They could have taken Pike out when he first appeared and saved themselves a lot of trouble.
A: It's a game...you cannot kill the final villain until the last dungeon! Ivy's just very genre savvy...
A: She was afraid of being discovered by the others, since it's obvious Ivy is worried about what people will think about her, however she knew there was no other option once Ark proved unable to break Pike's barrier and nobody wanted Halley and Emmy to sacrifice themselves.
A: Unlike the other battle forms CIMA builders go into, the sword (and perhaps other weapons depending on the user or the person who is going to wield the weapon) can only be transformed into if the one who is going to transform truly trusts the one who will wield the weapon. Ivy didn't trust Ark for the longest time, and while she trusted Jester as a fighter she probably couldn't trust him with her identity.
A: All three theories combine to make her thinking process.
Q: Does Ivy have a battle form of her own, or is the sword transformation her only one?
A: All CIMA only have one battle form, and either choose whether to transform into a weapon or beast, or it's based on the power of the individual builder.
A: Her sword form was based on her Trust for Ark, so she also has a battle form she can use individually. However, she isn't using it because it would compromise her identity.
Q: Why does Pike fight Jester with a sword, yet brings out a huge machine to fight Ark?
A: Pike's as genre savvy as Ivy is, and knows the final boss needs to be impressive. Though he might want to read up on the part about how final bosses always get licked by the hero...
A: Jester and Pike go way back, so there's no need to be showy around him; it would be more humiliating to kill his rival with a sword. As for Ark, it was all a show of power.
A: Maybe Jester couldn't break Pike's barrier either, but since Ark could with Ivy's sword, he had to get something more powerful.
A: Pike might know that a builder transforming into a weapon is powerful, and while Ark himself isn't cause for fear the weapon Ivy became is. Best to take precautions.
A: Even though he scoffs at a human and CIMA showing Trust for one another, Pike has heard of a legend speaking of how powerful that force can be. So he tries to use all the weapons he has, as well as psych Ark out in order to prevent their combined power from being effective...
Q: All of the builders simply fade away when they die, and don't fall unconscious first. So why does Ivy simply collapse to the ground after the final battle?
A: The designers didn't bother to actually think up a reason since the scene was written for drama purposes and to show something about Ark and Ivy's relationship.
A: There are different breeds of CIMA builders, and Ivy is the only representative of that type we see.
A: Ivy has had her body altered in some way to better fit in with the humans.
A: Her exposure to the atmosphere in the human world for a long period of time changed her physiology.
A: She was changed because of her strong desire to fit in among the world that adopted her.
A: She is, in fact, only half CIMA, having a lot of human traits body wise and the CIMA ability to shapeshift. Though since that probably wouldn't matter when talking with those who are scared of her powers, she doesn't bother to clarify.