Have you seen The Why of Fry? In the episode, Nibbler is explaining to Fry that he's the most importanat person in the universe, and that they need his help. And while Fry is debating wether or not to return to the future while hiding under the desk in the cryongenics lab, Nibbler asks Fry if theres anyone in the future worth going back for. Fry mentions Leela, and Nibbler mentions about her being 'the other'. He promises Fry that if he goes back into the future, he will help Fry along with Leela.
So, as he knows that the PE crew are going to be going to Vergon 6, where all them doomed animals were, he goes there and poses as a cute semi-unintelligent life form, which Leela then adopts as a pet. Nibbler then becomes part of the family almost, is able to watch over Fry until his time came to save the universe, and could also help him out with Leela. Thus by handing the flower to Fry after they'd just saved the universe in The Why of Fry. Fry walks in the door with the flower, not really remembering how or why he has it in the first place, and hands it to Leela to cheer her up after her disastrous date the the Mayors aid. Leela, touched by this, kisses Fry, and Fry considers this a minor victory
And Nibbler didn't break his promise. And thats
probabaly a slightly roudabout way of explaining why he was on Vergon 6