: I saw that happen so many times and I wondered the same thing as you did. I
: don't remember anything being mentioned that Keyes and Johnson were a
: couple? I haven't played Halo 2 in a while, maybe I'll fire it up this
: weekend and check it out.

At the end when Miranda crashed her pelican onto the platform, Johnson asked her to shoot him and she couldn't. Truth shot her and Sarge ran to her. He gave up fighting and let Truth push his hand onto the big button. https://youtu.be/jBiHMsKX1AM?t=1437

When you eventually fight your way to the platform you see sarge cradling Miranda and you have to deactivate the firing sequence. https://youtu.be/jBiHMsKX1AM?t=1625 if Johnson had been himself then he would have already stropped the sequence himself, instead, he is holding keyes.

When sarge is dying after you kill spark he says, "don't let her go" or "don't ever let her go" or words to that effect. https://youtu.be/jBiHMsKX1AM?t=2384

As an aside...

a bit later, Cortana tells Chief that she is so sorry for him (because of Sarge's death).

Compare that Cortana with the Cortana that mocks Vale's mental health issues in Halo 5. Two different characters.