After the guards clock out and leave, there's a blur too fast for the cameras to pick up, and each of their replacement are quickly knocked out before they notice anything is happening. Barry takes their ID cards and comms just in case they wake up, and then phases through the door.

Quick use of one of the ID cards once inside means the alarms in this section of the base won't be going off anytime soon.

"I'm in. What's next?"