Project X didn't enter the same way the Avengers did.  The way they took would take twice as long to reach the heart of the base as hers did.  And they already had a five minute head start.

She stopped to clip on the muzzle, then sprinted down the hall, barely tiring, thanks to her genetic makeup.

Slowing outside the door, she made sure she was as ready as possible to fight if the Avengers were already there.  But when she opened the door, the man from the alleyway was there.

"Project X," he said coolly, walking over to her.

She nodded her head in deference.

"I see that you have succeeded in assassinating Steve Rogers."

Again she nodded.

"But Captain America still lives!" he yelled, slamming her backwards against the wall.

"Da.  But he and three others are on their way to here.  I've been held in a prison all this time and have finally been able to even be near enough to him."  She shoved him off.

"How did you escape?"

"I didn't know the Avengers were careless enough to leave me and the key to my cuffs alone."

The man cracked a smile, an almost ugly thing.

Then the two members of HYDRA, one willing, the other born into it, were rocked off their feet by an earthquake and huge roar.

"How many Avengers did you bring?" the man asked, aiming a gun at her.

"If you shoot me, you'll die.  You're no match for them."

"We have fifteen minutes.  In the chair."

She shuddered but did as he said.  The metal arms moved down to her temples and the shocks began.  Once that was over, he started the trigger words.

By the time he was finished, she had gone from deadly super soldier to deadly super monster.

She was told three words.  "Kill them all."

Then the man fled.

Moments later, a huge green mass dropped to the floor with a load of snow, stone, and concrete.  The Hulk paused to roar again, then lunged at Project X.  She stepped neatly out of the way and prepared for the next heroes to drop from the ceiling.

That next hero was the Falcon.

But before she could fight him, Hulk roared again and she had to deal with him.