The word 'partners' is quite a powerful one. It can mean quite a lot of different things, actually, depending on the context.
When Captain Jack Harkness hears the word 'partners', he thinks of a friend. He thinks of someone that you're so incredibly close to that you can finish their sentence. The sort of a person you can depend on to always kick the bad guy's arse with you. The sort you can appreciate the company of, even if you're just hanging around talking. The sort you can go on wild adventures with, and come back home that afternoon bruised and happy. The sort that, if you're working with them, it really doesn't seem like work. The sort you're so incredibly close to that you could overtake the world together if you so chose. But you wouldn't, of course.
When Captain John Hart hears the word 'partners', he thinks of sex. Just the word itself turns him on. Just sex, in all it's variety, in men and women of all different species. He doesn't care who or what with, really… sex is sex, and John accepts it as a fantastic part of life. 'Partners' was just a coupling of two people that felt lust and desire for one another, and occasionally love. Behind his eyes, he sees the two people – one of them usually him – just fucking each other out of their minds. And it's good.
When Mister Ianto Jones hears the word 'partners', he feels safe straight away. To him, it is a term of closeness, and happiness, and comfort, and absolute trust. A partner to him brings peace and hope. A partner to him is someone you'll love always and forever, no matter what they do. That special someone whose limbs you can warm yourself within on cold nights. The one that brings pleasure and pain and meaning to life.
"We were partners." says Captain John Hart. He thinks of all the nights that never seemed to end with Captain Jack Harkness. And he grins.
Captain Jack Harkness thinks about the shenanigans that he and Captain John Hart got into together. He thinks of the fights, and the freedom, and the conceited insolence, and… well, the sex, too. And he grins.
Mister Ianto Jones sees the nostalgic grins on both Captains' faces. He sees the esoteric laughs just waiting to burst from both of their lips. He thinks of a safe, happy place where the two Captains sat together, quite obviously mad about one another. And he thinks of how he can't quite get in.
"In what way?" asks Mister Ianto Jones.
"In every way." says Captain John Hart. He watches the pretty Welsh boy squirm.
The three glance around at one another. There's a bias in the glances… they're a jigsaw that Mister Ianto Jones doesn't fit… a unanimous, loving nostalgia that only the two Captains can feel.
And Mister Ianto Jones cocks his gun.