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> First off, there’s the Covenant, all that we learn in Halo 4 is that they are more disorganized and that they worship the Forerunners, but we never find out how exactly such a large force became so unified in this sort of belief right after discovering that they had been lied to for thousand of years about their last set of beliefs,
Isolating to the games alone, all we really know in Halo 4 is that Thel ‘Vadam and some of his Sangheili were allied with the UNSC after the Covenant broke. We don’t know how widespread that break was, and if there were factions that remained true to the Great Journey. As Cortana remarks: “A lot can happen in four years”.
John notes that the Covenant are more fanatical than others that they encountered previously, giving strong indication to their disposition. As well, in the crash site on Requiem Cortana translates a broadcast: ”“Non-believers walk the sacred ground. Purge the heretics, so that they do not foul the air of Paradise. The time has come to enter the Great Light. The Promethean awakening is nigh…our reward is at hand.” This tells what the Covenant are looking for, and they even name him; Didact.
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> we also never hear a single thing about Jul 'Mdama in Halo 4’s campaign, all we get about him are a few lines in Halo 5 and then he gets killed in the first mission, that’s literally it.
So far as the overall plot is concerned, Jul ‘Mdama is really unimportant. We don’t really need to know much more about him than we’re told; he’s the Supreme Leader of the Covenant, and Fireteam Osiris was given the clear to assassinate him.
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> Next there’s the Didact, and ancient humanity.
What we learn in the cutscene with the Librarian is all we need to know about the Didact, really. He holds a vendetta against Humanity, and composed them to fuel his Promethean army. He would have composed all humans if he could, and in the plot of the game that’s exactly what he attempts.
In regards to the Flood, so far as the “Mainline games” are concerned that’s junk information. It’s not important to the plot, and the specifics of it don’t really matter. All we need to know, which we do know, is that there was a war between Forerunners and Humanity, and the Didact hates Humanity for it.
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> Anyways, another problem with the Didact is that we never learn about the source or nature of his powers and probably the worst part about him is that they make it seem like he dies at the end of Halo 4 when in reality he dies in a comic,
What powers? And so far as the “Mainline game” plot goes, the Didact is a done deal. A player could consider him dead, never read the comics to learn what really happened, and it would make no difference. Either way, the Didact is out of the picture.
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> At the end of Halo 4 we saw the Master Chief having his armor taken off surrounded by UNSC personnel who were all looking at him in awe, and then at the start of Halo 5 the Master Chief is suddenly doing a ton of missions
Did we really think Halo 4’s Epilogue was going to be the end of it all? Narrative-wise, this is no issue. That scene was largely symbolic, and presents no conflict of information.
> and it just so happens that his old Spartan 2 buddies (who we’ve never met or even heard of in the games before) are here to help him out with these sudden new missions.
Spartans get sent on missions man, it’s kind of their thing. As for Blue Team, we learn enough about who they are though the game. Fred and Kelly mention them all being together in Boot Camp, so it’s clear from the beginning that these are Spartan-II’s who know John fairly well. In Evacuation, Osiris is talking about how they’re practically family. That’s all we really need to know for the plot.
> And all of that doesn’t even touch on fireteam Osiris,
Buck becoming a Spartan really needs no explanation, and without all the details outside the Mainline is about on the level with Johnson miraculously surviving. In fact, if Halo 3: ODST is discounted from the Mainline (as it has no bearing on the Chief), then Buck is an entirely new character. In the events of Halo 5 we learn backstories for all of Osiris; that Locke was formerly ONI, Vale is an expert on Sangheili language and culture, Buck was an ODST, and Tanaka is very familiar with the Outer Colonies and mechanics.
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> Wait a minute Halsey’s back? How and when did Halsey end up with those Elites?
The opening cutscene mentions that Halsey is in custody of Jul ‘Mdama. The how and why is unimportant to the plot, and if Halo Reach is not counted among the Mainline games, all we know from Halo 4 and Halo 5 is that she’s a UNSC scientist who created the Spartans and Cortana. Which is really all we need to know.
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> We may not have been told much about what the Covenant was but we did know based on Captain Keys’ comments about keeping Earth’s location a secret and the fact that the Pillar of Autumn just tried to run from the Covenant that the Covenant pose an exisistential threat to humanity. We also know this based on their desire to activate the Halo rings.
Granted you’ve a point on Reach concerning the plot of Halo: CE. It would still explain the urgency for their escape, as referenced in the opening cutscene.
As for the Covenant, though, there were a lot of questions regarding their motives and the gravity of the war. Questions that were answered in the accompanying novels, and of which explanations were lacking in-game. I can attest that I never really took the Covenant seriously until Halo 2, and that was before I was able to read any of the novels. In Halo: CE alone, they’re just some alien freaks who want to control a big Hula Hoop of Death. We know that we’ve got to keep Earth secret (how and why?) but we have no clue regarding the scope of the war.
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> At the very least we could tell through the Master Chief that they were super soldiers with advanced power armor that was compatible with AI who were tasked with extremely important missions and were considered extremely capable.
Compatible with AI? Yes. All the rest, not really. Frankly in the beginning I thought the Master Chief was literally a cyborg. As in, Robocop cyborg. I didn’t know that MJOLNIR was power armor, or what kind of “super soldier” he was outside of a cyborg. Games alone, we also were made to think he was the only one of “his kind”. Which presents all sorts of issues on it’s own.
Neither were these things explained in any of the following games until Halo 4, when we get our first glimpse at the Spartan-II Program, and the knowledge that Halsey abducted children for the Spartan-II Program and they’re mostly human, not robotic.
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> For Johnson yes, his survival was a mystery, but the Master Chief was literally on a ship with an AI that had coordinates to Earth at the end of CE,
We don’t know that Cortana had coordinates to Earth, or how far away Earth was, or if the ship that the Master Chief was on could even make it back. I remember being incredibly confused as to how Chief got back, relatively dissatisfied that it wasn’t addressed (again, before reading the books), but ultimately ignoring it - though it was a massive plot hole if relying on the games alone.