"You're thinking with your fists," Jane said sympathetically. She put her hands on his shield arm, and tried to ease him into lowering it. "Maybe we have been outplayed, but as long as we both live through this, there's hope."
The Doctor, strangely enough, was heartened to be put in a trap. Because she knew there was one thing you didn't put in a trap if one ever wanted it to have chance of working: her. The Master's trap meant there was an opportunity for another way.
"You're going to let her take me, and then you'll find me. I don't need Captain America, I need Steve Rogers. Whatever she has planned, it's not the end."
There were sounds of fighting all over the compound. The Avengers wouldn't be defeated, but it would be as tough as any battle they ever faced. Tony was cut off from his suit and the Iron Legion was used against him. He took Pepper out of the line of fire and set about trying to find a way to shut down the Master's control over the place.
The Doctor didn't have much time left, she wanted to use it wisely. She honestly had no idea how Steve was supposed to find them, perhaps their chances were slim but the Doctor would find a way to leave a trail of breadcrumbs, give Steve something he could use. Wouldn't she?
She kissed him. Part of her wanted to keep him distracted, keep him from fighting but it also just seemed like one of the best, last opportunities they might have.