He's showing his hand, he knows, but at the same time its so tiring to hide it all. It's utterly unfair to both Tony and Pepper, he knows that too - and this is why he didn't want to see them at all. Better for them to never know about this - ignorance is sometimes bliss, in the end.
When Tony announces his intention to leave Bruce quickly turns his gaze to him, grip on Pepper tightening again. "Don't," he manages, voice wheezing as he chokes back on the other half of what he wanted to say. (Don't leave.) "Stay. Please."
He tries to hide it, but its impossible to hide the pleading expression on his face, a sudden moment of desperation overwhelming him. He can't bear to see Tony leave again, not after everything, not after all those times. It's so selfish of him, but he simply--can't.