: I think Chief’s relationship with Cortana is intimate in a way that’s nearly
: unfathomable; when she’s in his suit, she’s essentially inside his mind,
: speeding up his reflexes. It’s always been difficult to portray in the
: games, but I do think even just the few months they spend together isn’t
: quite comparable to normal human to human interaction.

: Putting that aside, though, the Chief has gone through more awful crap in his
: career than most, and the span of the Halo games itself is almost
: unimaginable when you consider how much he’s done, how many crises he’s
: narrowly avoided dying and saved humanity again and again and again.
: That’d wear on anyone.

: I’ve always disliked Nylund’s portrayal of Chief, because I think whatever
: its intents it just came off as whiny, for lack of a better word, but it
: definitely displayed the weaknesses of Chief’s character. Or take Chief’s
: nightmare awakening from cryo in The Flood—terrified of becoming powerless
: to defend others. There’s always been chinks in his armor. It’s not
: surprising to me that they’d become exposed.

It's what I was going to mention on the first paragraph, but you also bring a really good point in the second. Cortana had been inside of his mind, she was the one person that truly understood him. Losing Spartans was devastating enough as it was, but to put it in perspective: One of John's dreams involve "the blue woman", his first mother, Halsey, and Cortana.

The people he has cherished the most in his life. For him, Cortana was a part of Halsey, and the intimacy he got from her and the truth about his emotions was one unlike any other being. The poem Connectivity of Halo Evolutions describes their relationship perfectly, and though I loathe to praise Karen Traviss due to her Kilo-5 Trilogy, Human Weakness described incredibly well the attachment the two of them had towards eachother.

Losing her? He's not only failed his mission. He felt he's failed Keyes after his orders to protect her from the enemy, Halsey for being a part of her, and Cortana herself for the things they got to share that no one else did, especially after doing things no other Spartan was expected to do.

Likewise, as mentioned, only now he's starting to get cracks in his armor: He got to see what a combat skin class twelve is like in the form of the Didact, the UNSC is already planning to replace him with the SPARTAN-IV, ONI has gathered too much power and is committing crimes in the name of humanity, Halsey herself has been imprisoned for crimes against humanity and gone rogue...

This is why I like Cortana but I don't want to have her return: These sorts of things are going to drive the Chief into very interesting places. Pull the rug from below a character, and you see what he's made of.