All that righteous indignation wasn't hard to read and, sarcastic as Jessica tried to come off, there was too much truth in what she said for Nick to deny it. That would just be an insult to her intelligence. They both knew how much worse things would've been for him if he'd told her the truth. It wasn't really a good time to agree with her, either. Any hint of 'I told you so' would likely earn him a trip out the door or worse than a slap. Instead he just shrugged again, with less hostility, and relaxed his defensive posture.
When she spoke again he nodded, thoughtful, glad she'd offered the information before he had to ask for it. Two years, that was a long damn time. Here was that guilt again, rearing up its ugly head to remind him of just how colossally he'd failed her. Nick couldn't bring himself to even feel betrayed anymore, this wasn't her fault. At least, Nick consoled himself, they'd started whatever they'd had before all that. They'd genuinely had something and it wasn't just some ploy by the Contessa to keep her enemies close (which Nick had, if he were being honest with himself, suspected). Knowing that was actually a relief.
"Val can be a real bitch," he said simply with his own sardonic smile to remind her that she was in good company here. Nick understood; Jessica wasn't the only one susceptible to the manipulation of HYDRA, and the former Director of S.H.I.E.L.D. didn't even have mind control as an excuse. All he had to blame for that was maybe his heart, and definitely his dick. Dwelling on his mistakes wouldn't change them, and wallowing in self-loathing wasn't going to help Jess. They both needed to move forward from all of this shit.