I agree that Scully is planning to kill herself. But, I'm not sure by the end that she will end up following through. Mulder's reaction to her confession is absolutely in character, I thought. As he begins to understand what she is saying, he pulls away from her, but almost immediately reaches back out to her like he is never letting go.

He doesn't touch her and she waits to be unmoored. Soon, she thinks. Inside, the telephone squalls.

She strikes him once on the sternum and starts to crumble. His hand stutters against her shoulder and she backs down, mumbles, "I have to go," but he snares her. "I have to," she says.

"No. Scully," he says then, his voice stretched and hoarse as he begins to understand. His embrace is hollow, first, then fierce enough to choke. "Scully, Scully," he whispers.

I feel like you can see the burden of the pain shifting, not that that makes it easier. So sad.