"Is it... you?"
What if he had found out about the truth? What if he had seen him too?
The young cop with his head smashed, covered with blood, staring at him in the dark. Every time Sam looks into those familiar eyes he can see a body and a soul ripped and torn apart, frozen, lost in time and asking for answers, 'why? Why did this happen to me?'. He now knows the unacceptable truth but doesn't tell Gene because, well, how can he? It is unbearably painful enough for him so how is Gene supposed to deal with this? He can't hurt someone, with such cruelty, who's always been there for him. Gene has a life here, wherever 'here' may be and he lives that life without fear nor regrets to protect others. And there's no reason why he must go through the pain of knowing such unfair, terrible truth.
(ATA s3e7)Gene: I asked him what was wrong, he wouldn't tell me, he said he couldn't tell me... He said he wanted to leave... I asked him why, he said it would be better for me if I didn't know.
So Sam decides not to tell. He just leaves not only because he knows he has to, but also because he wants to protect Gene at all costs, even death. After all this time, at last Sam realizes it was Gene Hunt who saved his life and this will be his chance to return the favor. And it'll be his one last gesture to save someone who means the whole world, no, life itself to him.