s2e8) The pain in his eyes when he desperately tries to defend Gene. Standing on the very edge of the cliff, where his whole life is becoming a lie and his sanity is at risk. Where everything he fought so hard for has vanished in a second. Among all the questions rushing through his mind in that moment, the first thing he asks is “what’s going to happen to Gene."
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.
(Ashes To Ashes 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 favour. And it’ll be his one last gesture to save someone who means the whole world, no, life itself to him.