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Originally Posted by Skyblade
First: Who or what was the Great Intelligence?
Rather than boring you with paragraphs on paragraphs, I will supply a link to the Tardis wiki, a fountain of information for questions like this.
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Why did he hate the Doctor so much (seriously, three defeats is enough to make him destroy the universe for revenge)?
It wasn't trying to destroy the smurfing universe. Don't be dramatic. It was trying to destroy the Doctor. Also there were far more than three defeats.
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How did he survive as a disembodied mind for so long?
It was a disembodied intelligence to begin with. It's also a member of the Cthulhu Mythos (specifically, Yog-Sothoth) according to expanded universe materials so basically expecting it to obey the laws of life on this planet is beyond ridiculous. Obviously it has powers beyond the powers of Earth life. This is far from unprecedented; the monster in "Midnight" is never even depicted onscreen and we never learn even a single detail about what it is or how it works, but it manages to control a human woman and the Doctor. This is far from the only example in the series' history.
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How exactly was he trapped and wanting to be "at peace"?
I'm not even sure what this question is supposed to be asking.
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Second: How did he control his non-entitous minions when he wasn't possessing them?
The same way it turned the Whisper Man into Walter Simeon. It's a disembodied intelligence. It is only using Simeon as its avatar because humans (and Time Lords) respond to human forms. It's a disembodied intelligence with the powers of telekinesis. By linking the Great Intelligence with the avatar it is possessing, you are not paying attention to the way it actually behaves. The avatar is not the Great Intelligence; it is merely the Great Intelligence's avatar. Moreover, it is pretty clearly possessing all of the Whisper Men; Walter Simeon's form is simply the only one it turned into a recognisable human form. This is how the Great Intelligence has worked for a long time; it was controlling all the Yeti robots in "The Abominable Snowmen" as well.
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Why did they collapse to nothing when he shattered their form, yet Strax's blow was immediately healed?
Pretty obviously they collapsed when the Great Intelligence shattered them because it was no longer holding them together, and Strax's blow was immediately healed because it was holding the one he struck together.
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Third: How did TGI learn of the Doctor, his secrets, and his history?
Obviously it happened offscreen. Do we really need to be shown the way the villain learns of every single aspect of what it uses in its plans? Because that would be tremendously boring storytelling. It doesn't advance the plot in any entertaining way. A disembodied intelligence pretty clearly has a wide range of ways to gather information, and it's not particularly necessary for us to see it learn things that it is going to use in the future.
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How did he grab three people from 1800's London through spacetime to the Doctor's grave? If he's capable of temporal manipulation, why did he need to access the Doctor's grave in the first place?
The psychic link between all the people in the 'conference call' is pretty obviously what enabled it to move them across time. It can't just move anyone anywhere; and more importantly, it can't move itself in time. Being able to travel in time directly on its own would give it the ability to wreak far more havoc on the Doctor's timestream.
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How did he know what the grave contained or how it would work?
Again, it had obviously been given the information offscreen.
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Fourth: If the Silence were organized specifically to prevent this from happening (and also seemed to know exactly where and when it would happen), where the frell were they when they could have actually been useful?
The Doctor had defeated them to the extent that they would be terrified of ever showing their face to any human that existed after 1969. Do you really expect that they could possibly do anything where any human is present after such a crushing defeat? Because if you do, then you weren't paying attention. The Silence couldn't show up because Clara (and probably others in the party) would "kill [them] all on sight". In fact, for all we know, they did show up and they were killed, but because the party stopped looking at them they forgot about it.
A lot of your questions are answered in the wiki article I linked or in the article about the episode.
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The Great Intelligence is the Master. It explains his knowledge of time travel, his knowledge of the Doctor, pretty much everything about his motivation. How exactly he controls the non-entities is a bit of an unknown, but we could believe it of a character who was actually built up and developed to be so clever and smart, and also one so broken. It would even explain the disembodied mind thing, as the failed resurrections and multiple destructions have already done some really weird things to him.
It would also explain why an entity capable of living forever and manipulating spacetime would want access to the Doctor's tomb. Getting access to everything that is the Doctor and manipulating it directly is perfectly in character. Even though he doesn't need to do it, he would, because it's malicious and has that personal touch that the Master loves oh so much.
While it's possible that the Great Intelligence is the Master, it would also mean the Master is Yog-Sothoth, which is highly unlikely since the Master is identified as a Time Lord, and has been known as a Time Lord since at least childhood if not infancy. It would mean that Yog-Sothoth has been running a very, very long con, which is possible, but unlikely because it would make for shoddy storytelling.
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Get over River Song already. Geez, I am sick of that Mary Sue.
River Song is far from a Mary Sue.