So Looker returns and rents a building in Lumiose City. He poses as a Detective (Apparently we aren't supposed to know he's a member of the International Police) and simply, you become his detective partner, you help a homeless girl, she becomes the assistant to looker, but she's also the leader of this gang, but the gang become good, then it turns out Emma gets a job with Dr. Xerosic who puts her in this robotic suit which controls her under a name 'Essentia' and steals Pokémon. In the end, Xerosic gives in (He's actually much nicer than you'd think in the main story), Looker reveals his true identity, reveals he's leaving, Xerosic goes with him to be arrrested, Looker gives you his name 'Looker' (as it's not his real one but we never get his actual name) and Emma becomes the head of the Detective Bureau. This all takes place in Lumiose City.
It's actually a really good post-game story. Also, Malva, the E4 member, reveals she used to be a member of Team Flare. You battle her but she only has her Pyroar.
I loved the addition of this, as it gave more of a story added on. I just wish there was more postgame storylines like this. My thoughts, is that in a potential sequel, Emma returns possibly older. It's nice to see Looker again too! I suspect this also confirms that XY are set after all other games (Not completely sure though)
XY do indeed take place after all of the previous games. BW/B2W2 came after the first four generations, and there is a person in the Pokémon Center on the northern side of Lumiose who mentions what Team Plasma tried to do in BW/B2W2. So, chronologically, XY are the futuremost games in-universe.