WARNING: The following contains spoilers for X-Men #16 by Jonathan Hickman, Phil Noto, VC's Clayton Cowles & Tom Muller, on sale now
The X-Men have reestablished themselves as the future of the mutant populace, with Cyclops and Jean Grey leading the team into victory against the forces of Annihilation. Even with powerful positions dangled overhead, the two classic X-Men chose to instead stay with the team they helped form.
In X-Men #16, Cyclops and Jean Grey were just offered positions onto the Quiet Council, but both turned them down to instead focus on the future of the X-Men as an organization.
X of Swords left the Quiet Council dealing with its first change in the roster since its formation: at the behest of the rest of the council, Jean was forced to vacate her spot in exchange for taking part in the final battle of the conflict. Meanwhile, Apocalypse was at the center of the entire event -- with much of the impetus for the storyline being his attempts to reunite with his family in Arakko. With his mission successful, Apocayplse volunteered to become the Krakoan presence in Amenth -- giving up his seat at the Quiet Council in the process. This leaves the most powerful governing body for Earth's mutant population with two empty seats.
Hoping to stave off any potential drama as the Council debates who to bring into more powerful positions, it's revealed in X-Men #16 that Xavier and Magneto have actually been working behind the scenes to garner enough support for their chosen representatives: it turns out they want to formally bring Jean back into the fold for the Summer Branch of the Council after her resignation, and that they want to give Cyclops the seat in the Autumn Branch that once belonged to Apocalypse. This would cement the X-Men's control of the Quiet Council, giving veterans of that team a majority in the ruling body. However, despite the power it would bring, Cyclops and Jean both turn down this offer.
As both heroes explain, they truly believe in the importance of the X-Men -- not just as a team to protect their home, but as an ideal to lift up the spirits and hopes of Krakoa as a whole. It seems that the pair will be putting their full energies into turning the X-Men back into a premier superhero team, designed around protecting the island nation and helping shape the future of the world. They want the X-Men to act on behalf of Krakoa, not merely to be in charge of the island as the Quiet Council are. For that to remain true, Cyclops and Jean must maintain some degree of separation between the leadership of the X-Men and the Quiet Council. While Cyclops reaffirms that as a Great Captain he'll remain at the service and command of the Quiet Council, he genuinely believes the X-Men need to be a separate body.
It's a powerful reminder of what kind of role the X-Men can really play in the future of Krakoa. Cyclops adds that they'll be holding elections to decide the X-Men's new roster, leaving the future of the team in the hands of the Krakoan citizens. It's a powerful step by Cyclops and Jean that will help strengthen their roles on Krakoa, while keeping the pair at the head of the X-Men.