I love how people here are so threatened by the idea of two mature, consenting adults who have known each other their whole lives and are also best friends possibly
being in a healthy romantic relationship. The horror...
Simply put, the depth of their bond really goes down into the roots of John-117 and Kelly-087's characters. They've been together for 35 years almost constantly both on and off the battlefield. In fact Kelly’s partnership with John is the longest standing relationship that exists for either character in Halo canon. As the prologue of ‘The Fall of Reach’ (the very first piece of Halo fiction that was released to the public) firmly establishes Kelly’s place as John’s right-hand Spartan and confidant. Their interactions with each other are also definitely the most emphasized and unique among the members of Blue Team. We’ve seen this evidenced throughout Halo canon many times over the years - particularly through moments like Kelly giving John a special ‘Spartan smile’, and later when John confronts imminent death from Hunter cannon fire strictly to protect her. They think about each other quite often when separated, with Kelly showing particular concern for John’s well-being. And Kelly is the only person whom John has ever referred to as being beautiful. You don’t see actions like this from either of them directed towards anyone else.
I have actually compiled a summarized list of moments from the Halo books and additional official media that cite all the times we’ve seen evidence of John and Kelly’s relationship given particular attention and how that could be considered at least a basis for underlying romantic feelings:
Now all this could just be played as how the two are best friends that have been through a lot together. And if the relationship between them stays that way, that would still be awesome because their friendship is inherently awesome. But if it just so happens to progress into something more as Blue Team’s story goes forward, there’s definitely a long-standing and canon-based reason for such a development to potentially occur. Now is it likely to happen? Probably not. But if it did it, certainly wouldn't be unwarranted or unhealthy. That's all there is to it.