After a brief stint helping Angelus get back on its feet, Carpenter takes on a leadership role in the Order of Enoch. I'm assuming his duties will involve managing the martial side of the Order, overseeing the training and management of the Order's "soldiers."
He never quite recovers from the near-fatal resolution of the final battle. While his spirit never falters, his body remains frail, his hands almost unusable. His role in the Order is pretty much administrative, since he can't physically do much. All through this time, Elaine is at his side, supportive and caring.
His daughter Elizabeth is one of his main worries. He can sense that the Entity left its mark on her soul and has opened a path to the dark powers they wield. He asks Jama to help oversee Elizabeth's training in learning how to cope and control these abilities. He gets some flak from the more conservative members of the Order, who see Elizabeth as one already lost and thus irredeemable. Needless to say, this does not foster any warm feelings in her regarding the Order and continues to be a sore point between her father and she.
At the start of the campaign, Carpenter's health is continuing to diminish. The general opinion is that he won't last much longer. He's still plugging away, though, waving away any offers for him to retire and rest. Elizabeth hasn't seen him in more than a year, and the last time they saw each other, the air was filled with so many unspoken and unresolvable issues that nothing much was actually said.