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:
Spoiler:
ShowThe Fall of Reach: The prologue establishing Kelly as John’s partner and close friend on Blue Team (a trend that would continue throughout the book and in later fiction for the majority of Blue Team’s missions - from Victoria to Sigma Octanus IV). John being enamored by Kelly’s speed on the second day of Spartan training. John offering to be the rabbit in Kelly’s place during a wilderness training exercise. John taking note of Kelly’s beauty (which he never does in regards to anyone else before or since). The two of them having a playful conversation during their first official mission. Multiple instances of ambient physical contact. Supporting each other in the face of Sam’s death. John picking up on Kelly’s smallest signs of worry when RED FLAG is scrubbed. Kelly offering to lead the dangerous space-op in John’s place.
*Fall of Reach - Comic Adaptation: Kelly appearing as a prominent figure in John’s dreams. More instances of playful banter and poignant moments of closeness between the two.
(*The comic obviously is not a 100% faithful adaption of the original book - but the fact that it does still take the time to build up John and Kelly’s relationship even in this condensed version of the story is something to be noted. Particularly since it was written by one of the lead writers for 'Halo 5’.)
First Strike: John returns to Reach strictly to find out if any of his Spartans are alive, in spite of the extreme tactical risk. His reunion with Kelly culminates in a uniquely intimate 'Spartan smile’. Afterwards he makes a last-ditch attempt to save her life when she is severely injured by Hunters - by putting himself in a completely prone an vulnerable position that would’ve lead to his own death as well should the Hunters have fired again. Most importantly, he is willing to make that sacrifice for her in spite of the fact that Dr. Halsey and Admiral Whitcomb (two extremely important people) were in their party and still in need of protection. He also continues to further prioritize Kelly’s safety and the need to get her medical attention above all else during their escape from Covenant forces. And after Dr. Halsey absconds with Kelly in a stolen spaceship, John is notably worried about her.
Ghosts of Onyx: Kelly’s primary question (second only to an inquiry about their current location) after regaining consciousness on Dr. Halsey’s ship is whether or not John knows knows where she is and what is going on. And later, after being reunited with Fred and Linda, she openly asks the others if they think John is alright.
Glasslands: Kelly has a conversation with Dr. Halsey where she reveals her worry over whether or not John is alive and well. Chief Mendez notes how this is something that really must be weighing heavily on Kelly’s mind for her to talk about it without being prompted first.
Halo Evolutions: John thinking about Kelly and how she would be impressed with how fast he sprinted over an open battlefield in New Mombasa (this is also the only time in the whole book when another Spartan-II from Blue Team is referenced by name).
Halo Legends: John desperately calls out to Kelly when she sacrifices her own momentum to get him onto the Covenant ship when floating out in space, and afterward he noticeably pauses and contemplates the possibility of just having lost her (something he did not do for Solomon, Arthur, or Fred).
Halo Escalation: Kelly and John immediately fall back into their positions as Blue-One and Blue-Two. And Fred, who technically should be in charge, does not even attempt to contest this and literally takes a backseat to the pair. A point is also made to show that Kelly specifically is in danger before John attacks the Didact with a combat knife.
Other: Kelly’s official character biography on Halo Waypoint takes the time to note her close relationship to John (personal and working) no less than 3 times. Them being each other’s closest friend was also included in a character summary that was published in Game Informer’s exclusive coverage on 'Halo 5’ - the information for which was provided directly by 343 Industries.
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.