Odona explained everything.

"We need the disease your body carries, to lower our population."
 
Kirk nodded.

"I see."

"Overpopulation leads to disorder."

"Yes, well. Disorder must be quelled by any and all means."
 
Odona picked up a hidden phaser.

"I'm glad you agree."

"How could I not?"

"James Kirk, will you tell me something?"

"Of course."

She held up the phaser.

"Why did you--aaahhahhhh!!!"

Kirk's knife met its mark. Odona fell over, quite dead.

"You can come out, now...the game's up."

As they always did, a group of impossibly strong pasty-faced men with perfectly straight hair moved the walls away.

"Well done, Number One!"

Again Kirk faced the regal-looking man, mostly bald, who was his sworn nemesis. He almost spat at him.

"I am not a number, I am a Federation citizen! Section 31 can't hope to change...."

  The man looked down at the sleeping Kirk, and smiled. His Anglo-Gallic accent made him sound all the more like a kingmaker.
 
"Invisible Gas, Number One. Let us see. The Nexus failed, The Tholian  Interphase failed, BOTH rehab colonies failed. Heh. We even blew up your ship, and killed your son! What to do next, after uncounted missed chances? I shan't last much longer without results. Ah, I know. On 'Veridian', we fought as brothers. But brothers can be lost, Number One. You know that better than any."

The Section 31 agent turned to two women, a tall redhead and a gorgeous brunette.

"Drug him and put him in the proper frame of mind. Its time he went back to that first five year mission. Physic, your precious brat should finally prove of use."

----------------------------------------------
 
When Kirk awoke, he saw he was again on the First Enterprise. He had long since learned not to trust the people who walked and talked and looked like his friends.

He knew this day. Sam and Aurelan were dead, and it was left to him to explain this to a Peter who had just come out of his coma. But the boy looked taller, lankier, and not really at all like Sam. But with all they had done to him, could he really be sure what his kin had looked like anymore? For that matter, could he know anything? Of course he could not

With 'Spock' and 'McCoy' flanking him, he feigned a smile as the boy awoke.

"Peter? Son, can you hear me?"

"Un-Uncle Jim? Mom--Dad? Oh, No! Please, Uncle Jim, tell me something, and promise you'll tell me the truth?"

Exactly like that horrible day.

"Of course, Pete. Ask me anything."

The grieving boy almost seemed to be fighting back a smile. Kirk knew, then, what his question would be.

"Uncle Jim?"

The Pause.

"Why Did You Resign?"