Halo has constantly been frustratingly close to being LGBT allegory, the point that I sometimes froth at the mouth when I think about it too hard.

Ignoring the big transhumanist plotline that was being built up from 2010-2014 with the now-abandoned Halo 4 plotline, Halo Spartans have always been very sort-of-trans.

See, until Halo Reach in 2010, Spartans were always depicted as a homogeneous force of tall, sage-titanium clad cyborgs. It was canon that every Spartan looked just like Master Chief... But Reach, being the first game to feature multiple Spartans, needed some way to visually distinguish them. Alongside the consumer demand to customize their guy, Spartans went from a faceless and interchangeable superasset to a gaggle of identifiable and traumatized people.

Oh, and they made the Spartans sexually dimorphic. Prior to Reach, changing your "gender" only changed your multiplayer voice.

But let's get back to the point: Spartans are agender. The books constantly reinforced that you can't tell who's who behind the visor unless you recognize their voice, you definitely can't tell their gender, and that Spartans almost pathologically lack an individual identity.

That is to say: There is no way for a Spartan II to meaningfully interface with gender, other than to use the pronouns their abductors assigned to them. "He" or "she" is about as meaningful as "117" or "woah big robot".

Throughout the course of the plot, very few of the Spartan IIs meaningfully gender through their character development. John doesn't become "more of a man", he just starts to struggle with the conflict between his existence as a pragmatic military asset and his existence as a person.

Yes: I am saying John Halo is a he/him agender asexual guy (with astounding mommy issues.)

I'm meandering, but that's pretty much it. It wouldn't make any sense for a Spartan to have a gender identity. They're not cis, trans, nonbinary, etc-- they're just simply not gendering. Sure, Halo is the pinnacle of gamer teenage masculinity, but the Spartans don't know that.

...

There is one other example. Halo 3 ODST introduces Nathan Fillion as "Buck", the most cisgender man in the world. He's an ODST, and he genders hard. Then, in Halo: New Blood, Buck (Nathan Fillion) becomes a Spartan IV, and his personal account of the augmentation is basically a gender transition. He notices changes due to his "second puberty" (I'm pretty sure he uses that exact phrase in the book), his voice changes, he has mood swings, and yes, he is excited to have sex with his changing body. (That's pretty much it, I had nowhere else to put this.)