Since Pokemon Red and Blue, there's always been some treacherous villain up to no good, and it's always been up to you to stop them, and set things right. Pokemon X and Y introduces a team known as Nucleus, who wear militaristic garb, while the admins, who are also scientists, wear lab coats.

Team Nucleus' yearns to 'dive deeper' into the genetic makeup of pokemon to uncover the mysterious truth behind them. They believe that with their findings, they will change the pokemon world. The leader known as Diena, has other intentions.

Your rival, Gene, is a goodhearted person who fights for what he thinks is proper justice, but the fact that he's gullible and easy to sell, is an ugly conflicting trait.

Towards the middle of the story, after entering Rosassion City to acquire your fifth gym badge, you walk up, and right outside the gym you see Diena talking to Gene, who was one step ahead of you, and had just nabbed his own. This is the fourth encounter both you and Gene have had with Team Nucleus in the story. She leaves a lasting impression on him by telling him what is right and wrong is subjective, and that Nucleus aims to help the world by spreading newfound knowledge about pokemon and their true origin. A sub-plot involves your rival becoming a top admin for Nucleus, and it is your goal to help him see the error in his ways, as the future Diena promised seemed so good he failed to notice the extremes Nucleus would take to realize their dream.

On new pokemon, as in generation III, generation VI introduces 2 new psuedo evolutionary lines.

Armetarex is Dragon/Steel, and based on mechagodzilla, it's strongest statistics being in it's defenses. It's ability is Filter.

Domagon is Dragon/Fighting and based on a dragoon. It's statistics excel in it's offenses. It's ability is Infiltrator.