Leadership goes underground and works at getting communication, training, and supplies set up.

Leadership trains individuals who then go out to areas to assess, agitate for, and run groups in an area. Those individuals now have access to communication networks and resources maintained by the underground leadership while the individuals operate mostly independently of the central leadership.

Think of it in the same way the Palestinian resistance works right now. There are independent military brigades that operate within an area but are not micromanaged by central leadership outside of the brigade’s area of operations. Central leadership will get updates on what the brigades are doing and give the brigades whatever intel they can along with directing supplies but at the end of the day the brigades are mostly left alone to pick their targets. Central leadership can be compromised and the brigades can still fight, any one brigade can be compromised without immediately hindering the other brigades ability to fight.