Clint left the kitchen, not needing the look Pepper sent him to let him know he wasn't wanted in the kitchen.
Not knowing what was going on, but knowing it wasn't good, Clint did the only thing he could.
He called his best friend.
When Nat answered the phone, she said flatly, "I couldn't stop it. All I could do was get them out of there and warn Pepper."
"What the hell's happening, Nat?"
"The Winter Soldier killed Howard and Maria Stark."
Clint felt sick. "Oh, man."
"Without Barnes there, maybe Stark can see the killings for what they were."