Jean Grey was dead and Pyro had betrayed them. So Logan left and Rogue went with him. She would have stayed if Bobby had asked her to but he didn't so she climbed on the bike behind the Wolverine. Later at the Motel 6 he asked her why.
"Because Bobby needs to cry and he can't if I'm there with him. He needs time to mourn for John. He likes me, he really does, but he loves John." Loves, not loved. He quirked an eyebrow at that but said nothing. She shrugged, "I don't know." They slept then.
Driving again the next day she thought. Bobby didn't love Johnny with that angst ridden, passionate, pregnant pauses in seemingly innocent conversation love that only little, straight girls would sigh over, but he loved him quietly, solidly. What that meant exactly though, she didn't know. The touch was too brief, too fleeting and it was her own idealized naked body that she saw when they had kissed, but Bobby is 17 and that was to be expected.
Touching Johnny had lasted though, and St. John loves Bobby. Loves him in the 'fight like demons because Bobby accidentally froze John's wet towel to the floor where he had dropped it that morning' kind of way, in the 'playing cards until dawn under a blanket that Bobby was always terrified would catch on fire because of the flame Johnny balanced on his finger to give them light' kind of way. Johnny loves Bobby in the 'please let me fuck you hard and let me hold you sweaty and sticky close to my chest afterwards' kind of way. The kind of way that makes the little girls a bit squeamish about the whole deal because it isn't the clean, sweet, PG-13, boy-boy love that they like to pretend it is.
Johnny didn't leave because of Rogue though, this she knew with certainty. If St. John wanted to have Bobby for himself he could have. He could have made Bobby love him any way he wanted to. So no, he didn't leave because of jealousy or rejection. She guessed that he left because he just had a different path to follow.
They stopped for a smelly washroom and stale chips then, and Rogue smiled to herself in the spotted mirror.
"Marie, you want barbeque or dill pickle?"
"Sour cream and onion if they have it."
Later, that night in a motel much seedier than the Motel 6, she sat on his lap with her head on his shoulder.
"It's not good versus evil Marie, it's them against us. Don't you ever get so righteous that you think its o.k. to kill. It ain't. But sometimes it's gotta be done."
She cried then, but not for as long as she thought she would, and she felt better. She guesses that Johnny just thought it had to be done a little bit more.