Amanda Waller was tired if being eluded. She had been searching for this group of aliens that Mercer said were planning on destroying the planet. Apparently the only hope Earth had was this so-called Traveler, as she had put it. Waller has been starved for information ever since Mercer went off the grid.
She suspected that it had something to do with the identity of the also elusive Green Arrow, after all she knew Mercer knew the famed Blur's identity. She had hoped that that would come out with minimal encouragement. Now they had no chance to try to encourage her, minimally or otherwise, since she left leaving nothing behind at all except her piece, the knight. Waller knew she had done that on purpose.
She knew that was purposeful, she had trained her to well to suspect otherwise. She had trained her better than she ever intended. But between the training she went through with both Waller and Luthor she would be untraceable. That is unless she wants to be found, which is another story entirely.
Mercer knew more than she let on, but Waller knew. The alien was sloppy, the Blur was sloppy, Green Arrow, but Waller suspected that was for an entirely different reason. Nonetheless, while Mercer was careful, she wasn't careful enough to surround herself with people of the same mind frame, because those people were sloppy.
Though she was good enough to cover her tracks. The alien didn't own about her involvement with Checkmate, because in all honesty that'd be a one-way ticket to obliteration. But Waller did know about her involvement with the alien, which Mercer wasn't aware of. Because otherwise she probably would have withdrawn from the program entirely. And in Waller's mind that wasn't an option. Mercer's mind was a well of information that required great skill to crack, but once opened held enough information that would make even Waller quiver.
One of Waller's assistants had asked why she didn't just rat Mercer out. The answer to that was simple. Mercer had information that Waller needed and she had a sinking feeling that well of knowledge was unique to her. Which brings the train of thought back to coaxing the information out of her.
It was blatantly obvious that that wasn't going to happen anymore. No, at this point she wouldn't just hand the information over, not that it was likely she would in the first place butt the current situation promised that Mercer wouldn't hand anything over. There was always tried and true torture, but Waller knew that physical torture wouldn't work. Her upbringing wouldn't allow that. But maybe emotional torture could work, or in turn, the physical torture of someone she cares about. The difficult part was finding someone Mercer actually cared about. Oliver Queen was an option, an ex-flame. It was rather risky though, because emotional pain often causes hatred. And Queen put her through enough to justify hatred. So she might actually enjoy that, which certainly wouldn't work.
She could always go to the alien, turn Mercer in to them, just out of spite, and turn on them later. The difficult part would be getting the information that brought us to this thought process. Though it would feel really good to watch Mercer get tortured by the people, metaphorically speaking, she betrayed her country for.
This leaves termination. She betrayed her country. Besides, the risk of her telling anyone about The Castle or what happens in it is simply not worth it. Tess Mercer must be terminated.
The door swings open. "Ms. Waller, what are your plans for Mercer?" Waller's task force
leader, Stuart, asks. He was charged with leading the team in doing whatever Waller wanted them to do to Mercer, who he never trusted.
As Waller explains their job they move into the hallway outside her office. She explains that they have to find her and simply kill her. Stuart seems to have no objections.
The alarms sound and the roof caves in due to the arrival of the alien. Waller's smart enough to know she's about to die. Knowing this she spends her last thought, "Darn you, Mercer."