Shepard will be sent away for examination.

"We can't afford to risk something like this." Ashley decided. "We'll have EDI's body sent away for analysis and research."

"Ash, you're making a big mis-" Shepard began urgently. Unfortunately, she was cut off mid-protestation by Ashley, who raised her omni-tool and deactivated her.

The infiltration platform slumped down. Though she was unable to move her body or communicate in any way, Shepard could still recieve audio and video, as well as sensory output from throughout the gynoid's body.

So, although she was aware of Ashley's personnel escorting Traynor back to her post, and boxing EDI's old body up, Shepard was powerless to do anything to prevent her fate.