Blue Team and Team Osiris are Foils: Blue have known each other since childhood, never have their helmets off during a job, and always call each other by their first names. Osiris are a close knit but not familial team, regularly have their helmets off, and call each other by their last names.
The very first mission that the Blue Team, who are more tactical and pretty much a loveletter to the series veterans, have to take on is a UNSC ship controlled by and plagued with Covenant that ultimately undergoes a manual self-destruct at the hands of the Spartans. Even if it's a hodgepodge of various elements, it's fitting that it's just like old times to the point that one of the squad even remarks that UNSC reactor failsafe standards must have improved when simply trying to cause it to meltdown directly doesn't work as planned thanks to the automated cooling systems, in a nod to the Pillar of Autumn.
It even ends somewhat similarly; with Blue Team escaping on an experimental stealth ship called a Prowler and outspeeding the meltdown in a manner almost identical to Chief escaping on the Longsword from the destruction of the Halo installation in the first game.
343 pulling a Cliffhanger and having us wait for the conclusion to come in maybe two or three years may have seemed like a really douchey move, but then it hit me: They did the exact same thing that Bungie did with Halo 2: A massive cliffhanger that had us waiting eagerly for the next installment.
The trailers indicated that the central conflict would be about Locke pursuing Chief and them coming into conflict, but as is often the case, Trailers Always Lie - while this is similar to the marketing campaign of Halo 3 depicting a conflict that never ended up happening, there's another layer to this - the Arc Words to the marketing campaign were "Hunt the Truth". Playing the game itself uncovers the truth the trailers avoided.
On the trailers saying the Master Chief had gone rogue from the UNSC the story shows that the Chief is still loyal to the UNSC. However, the whole "hero goes rogue" angle still works perfectly well...if you substitute the Master Chief with Cortana.
Replay the game knowing the Warden Eternal is in love with Cortana, and Cortana is in love with Master Chief, and suddenly a lot of the dialog sounds like a Love Triangle spat, especially when Warden Eternal spitefully talks to Chief about him not being good enough for her, and his anguish every time Cortana pushes (or teleports) him away and shows affection for Master Chief. Then when Master Chief maintains a friendzone with Cortana, she acts like a Stalker with a Crush, vowing he will understand after she's done with her quest, and kidnaps him all to herself. There's a reason she screams pitifully "JOHN!" when 031 Exuberant Witness steals Master Chief away from her.
One could read into the relationship between Cortana and the Warden Eternal as evidence that Cortana isn't fit to rule over a galaxy controlled by A.I.s if she can't even reign in one. It could even be a sign of what her rule would be like if she succeeded.
Cortana is humming during the Legendary Ending on a Halo ring. Wait a minute — that's the tune 343 Guilty Spark hummed.
In the final level Exuberant Witness calls what's going on "Unacceptable", echoing Guilty Spark in Halo 3. It's a chilling reminder that while Witness isn't crazy, probably, for now, she could turn into another Guilty Spark later.
