<Not going into this kinda thing with most quests, as I believe the Saint-14 Quest was well explained in game (the only thing well explained in CoO), same goes for the Titan Quest and O Captain my Captain. I believe Enhance! is too boring to do an analysis of.
[b]Premeditation:[/b]
The quest starts with Ikora telling you that one of her hidden discovered the Taken trapping the Vex... before the agent "went dark" which I'm pretty sure means dead.
The Taken are creating Blights around the area, which make a nice field around them. The Vex become trapped in them and an Ensnaring Wizard does the rest. The Taken Wizard is responsible for creating the Blight and leading a localized operation which is part of a plan that spreads across the region and possibly the whole moon.
Later on we come to a room full of captured Vex. The Blights are soon replaced with portals, and when the latter disappears, the Vex are no longer there. The portals are to the Ascendant Realm in this case. The Ascendant Realm is where all powerful Hive and Worm Gods make their permanent home. It is also the residence of the Darkness, which is found deeper in the Ascendant Plane.
These portals are another form of Taking. In The Coming War in D1, Cabal were being Taken through smaller wounds in space. It does not matter, for the destination is the same. The Darkness corrupts the Vex and sends them back. It is also in this room where we find Ir Arok, Tongue of Quria.
Brief history, Quria is a Vex Hydra designed to deduce the Sword Logic during the Vex Incursion on Oryx's Dreadnaught. Oryx took it and gifted it to Savathun, his... cruel sister. The important thing to note about Quria is that it has a little bit of will left, meaning it has either a very loose connection to the Vex Collective or that it is more aware of what is going on.
Savathun is leading the Hive and Taken, but Quria may be second in command. More evidence of Quria's influence comes in when Ir Arok disappears and Elatiox, Beloved of Quria steps in. No matter, it falls like all the rest.
[b]Calculated Action:[/b]
The Blight has started affecting the Vex Collective as a whole. Even Asher can feel it. This sort of points towards Quria being connected to them, but it's a bit of a stretch. It mainly just means that the Taken have started Blighting the network.
Ghost mentions that the Blight on the floor and walls are being used as gateways to abduct unsuspecting Vex units. Not only does this prove that any Blighted surface can be used as a portal, but that the Blight itself is a gateway. This is further proven by seeing more captured Vex in the abandoned base. The Blights hovering over them slowly lower themselves and burst when they reach the ground. The Blight is absorbing any entities inside to transport them to the Ascendant Plane to be Taken. This also proves that the process of Taking is instantaneous from an outside point of view.
Erosus, Spawn of Quria, besides being further evidence of the latter's influence in this operation, is the only Taken Hydra we've seen in-game and the second Taken Hydra overall that uses the basic Hydra model, the first being Hephone in D1.
Asher mentions that Taking the Vex is "suicidal" because Vex subroutines are capable of overriding the corruption. Ikora says it's a calculated risk and that the Taken are merely building a disposable army. I believe there's more to it.
While the latter turns out to be true, notice that every major Taken enemy in this quest has titles that end with Quria. Remember that it has some will left intact. Perhaps it's playing the long game with a bit of Savathun's game trickled in.
[b]The Long Play:[/b]
The Taken army has entered the Pyramidion. Ikora brings up how close Oryx was to corrupting the Collective Mind. This is in reference to the missions Paradox and Entropy's Pinnacle, where the Taken infiltrated the network through the Vault of Glass and the Citadel.
The Pyramidion is another Vex hot spot like the VoG and Citadel. The Taken made a good choice. There's really not much to mention here other than the Taken forcibly opening a Vex gateway.
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I'd like to mention that "Savathun's Game" is trickery, cunning. What I meant by Quria playing a game meant that it was either convincing Savathun or whatever to take the Vex and make a noticeable move. She clearly knows about us, hell, she saw us through that glorified Security Camera called a Shrieker. If she knows, Quria knows. Perhaps it is trying to get our attention, or maybe it knew that the temporary army would fail because of us, which would leave that army roaming among other Taken, slowly purifying themselves back into normal Vex. At the right time, this army could be used to fight Savathun and the rest of the Taken under Quria's command. It's easy.
Let's also take into consideration Savathun's personality. She is much crueler than her brother, Oryx. Her initial goals in life were to take the "mother jelly" not to become a mother, but to live longer. Seems like an interesting idea until you consider the rest of what she's done. When Oryx, then Auryx, tried to make a deal with the first major enemy the Hive came across, the Ammonites, Savathun kill him. Nobody knew about their throne-worlds at the time. Savathun also tried to kill Auryx when the latter was going to get answers on how to defeat the Ecumene, the first and so far only non-acausal race to come close to beating the Hive entirely. Since then, her goal has been to steal her brother's abilities.
She came close a few times. She even sent Malok to steal it, didn't work. She also let the Vex into Oryx's Realm through Crota. She has known about the Vex for centuries.
The key to Oryx's full power lie in the Tablets of Ruin, a direct way to communicate with the Darkness itself. They are in his Dreadnaught, in Golgoroth's cellar... the latter is dead as well. Her brother is dead, while she may have loved him, his absence means her rise to power. Now that she has the power to Take, she may want to experiment, as Hive witches do. This could lead to careless use of her newfound abilities, and possibly how this Taken Vex army came to being in the first place.
This is also the second time we've saved the Vex from the Taken. I would say this leads to a Vex alliance, but CoO is kinda pushing that a bit back.
Also Ghost calls Taken Vex "scary Void robots" in Calculated Action. The 2 mentions of the Deep or its ability being called or referred to as "the Void" bring up something quite interesting. Especially when you consider the void's connection to the Nine. I'm telling you, the Darkness and Nine are related.
Anyway, I hope you enjoyed my lengthy ramblings on the subject of one quest that holds severe implications for DLC4, the Taken Queen (hopefully not actually called the Taken Queen).>
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Annnnnnnnnnnnnd now I have a huge hankering to go back and play Taken King