The Season Finale "Descent" by the end. Sidorov has captured Sam and Deeks and is using Electric Torture on Sam to learn if Quinn - Sam's wife Michelle - is a federal agent. Then it goes From Bad to Worse; Sidorov goes and starts on Deeks using a dentist drill. All Sam can do is watch as Deeks screams in agony.
It gets even worse if you look at it from Sam's perspective: he pretty much admitted earlier in the episode that he doesn't respect Deeks to his face. Not only did Deeks save his life from drowning, but now all he can do is watch and listen to Deeks' screams - which are echoing - and hope that the man that he said he didn't respect can find it in himself to fight through the agony and protect the woman he loves.
We see the aftermath of their torture in "Ascension". Deeks' mouth is covered in blood and when he awakes, he's practically begging Kensi to get him out of there.
"The Sound of Silence" has the LA team investigate the injuries of a Navy officer in Seal Beach, which turns out be caused by microwaves. Like the attacks on American and Canadian embassies in Havana, being affected by one can make you dizzy, nauseous and at most cases, can cause harm to your hearing.