Minifiction Time!
Regret
Human biology can only take so much pleasure. After an extensive period of receiving the same stimuli, over and over, the nucleus accumbens (the portion of the brain that receives stimuli and then decides if it should result in pleasure, pain, or addiction) begins to question the incoming information. It becomes suspicious that the body could be in a situation where it could encountering so much pleasure. In short: the human brain believes it is being tricked.
In an act of self-preservation, the brain will attempt to persuade the human to leave the area. To accomplish this, the ventral tegmental area begins slowing the flow of dopamine to the body. Dopamine, nature's "pleasure" drug, gives a human the natural high they experience during periods of intense pleasure or success. When this supply is cut off, the human becomes more lucid, and will thus become aware of any pains or aches that had before been ignored.
If this dopamine reduction doesn't cause the human to remove themselves from the situation that has been causing the intense, excessive pleasure, the brain takes a drastic step. In an effort to force the human away from the suspicious stimuli, the brain will activate the body's nociceptors. These "pain receptors" cause the human to experience intolerable pain. While helpful in advoiding dangerous situations, this reaction can be incredibly unfortunate for an individual unable to remove themselves from the source of pleasure.
Commander Shepard was experienceing this dilemma first hand. He had fought, as he had done against every enemy beforehand. The Geth. The Collectors. The Reapers. But this fight, this struggle, was something different. Shepard had consented to it. Looking back at it now, he doubted that he had ever made a more regretable choice. But who could have known that the slender quarian sitting atop of him could cause this much pleasure? And by extension: who could have known she could cause this much pain?