I do not own Code Lyoko or anything to do with it.
This is what I think happened at the end of Replika.
Everyone was walking out of the factory. Aelita noticed that Jeremie was walking slowly and looking at the ground. She slowed down until she matched his pace, and let the others get ahead of them. When they were out of sight, she placed her hand on his arm. He looked up to meet her gaze.
"Hey, are you going to be okay?" she asked, concerned.
"Oh, yeah, sure, Aelita." he answered. But she could tell he was still a bit unsettled, so she continued talking to him.
"Because you know that kiss meant absolutely nothing, right?"
"Right." he answered. He did know it. But he still couldn't help being jealous.
"I know we kind of made fun of you, but I really admire that you didn't freak out. I don't know if I could do the same. You really do have an open mind, you know."
"Yeah, yeah." Jeremie mumbled.
"Anyway, I'd much rather kiss you."
Jeremie didn't have time to be shocked what she said, because she gave him something else to be shocked about as her lips hit his in a kiss. She held his head, burying her hands in his hair, and continued to kiss him, turning his mind to mush, making him go weak in the knees. Her sweet presence filled his awareness completely, driving out his concerns and troubles. He was just content to be there with her. Eventually the kiss stopped and Aelita stood back.
"Come on, Jeremie, don't freeze up again." she said, smiling, taking him arm again. "Just walk it off."
Jeremie just let Aelita lead him forward, smiling slightly and blushing. He wasn't jealous of Odd anymore. Not at all.