Gambit and Rogue's first kiss came when the world ended. With Legion having thrown reality out of kilter by accidentally killing Xavier in the past before he had a chance to found the team, a crystal wave from the M'Kraan Crystal (the nexus of all possible realities) threatened to sweep over the planet, flashfreezing everyone in its path. It was, for all concerned, a time to seize the moment, to do one final thing before they died. In Gambit and Rogue's case, that one final thing was (to use Remy's words) "one helluva kiss".
Consequently, when time was righted by Bishop from the AoA, reality returned to the point at which it had been before the wave crystallised everything, leaving the couple liplocked. Rogue's powers had naturally kicked in at some stage, triggered by the contact, and she had absorbed his psyche, including several, unpleasant memories. Gambit was left in a coma, in which he passed three weeks. When he woke up, he found Rogue gone and feared that the secret to which Sabretooth had intimated was finally out of the bag....