Barry was startled by the sudden arrival of someone who was, at least to him, a complete stranger. So much so that he nearly fell off Len's lap as he abruptly disengaged from the kiss. Thankfully, his boyfriend was quick enough to steady him and save him from embarrassing himself further. He still had no idea what was going on, but Len had just pulled his gun - not actually the first time that had happened during a makeout session - and had it pointed at the newcomer.
He was caught between overwhelming embarrassment, genuine worry that Len was about to literally kill a guy, and still being decidedly turned on from their previous activities, and his body seemed unsure whether his blood was more necessary to his face or his dick. Needless to say, he had a very confused erection.
"Len, babe," he said, "chill out. You are not going to kill anyone because if you did, I definitely wouldn't sleep with you for...at least a week." Normally he'd try to at least pretend he'd never sleep with Len again if he murdered someone out of nowhere, but these were special circumstances. After all, Rip Hunter was most definitely cockblocking them. Taking a moment to think about dead puppies and the Reverse-Flash and Joe's disappointed face to calm down his erection, Barry turned enough that he didn't have his back to Rip without actually leaving his spot on Len's lap.
"Hey there, Captain," he said politely, giving the time traveler an awkward smile. "It's nice to finally meet you. Sort of curious why you're in our apartment. Without knocking. I'd apologize for...that, but really it was your own fault." He felt he was handling himself pretty well, considering how utterly mortified he was at being half-dressed in front of one of Len's teammates, who he'd never met before. Len didn't exactly help, stealing his shirt from him when he tried to grab it and put it on. Rolling his eyes, he grabbed Len's shirt and put it on instead. "Now, what did you want to talk about? Because I'd like to get that over with so I can throw myself out a window."