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It isn’t really that they break up. Breaking up is a tricky thing to do when you were never exactly ‘together’ in the first place. Language is a subtle thing at times, and ‘together’ holds a lot of implications that Dana doesn’t like to dwell on.
Some of it’s true, obviously. They live together. They sleep together at night and clasp their hands together when they go outside. They share soft kisses over breakfast and curl up together on the sofa in the evenings.
They had a baby together.
But they never get married. They don’t raise a family together, not like normal couples do. They don’t really even sleep together – in the subtle, implied sense this time, not the lying-next-to-one-another-at-night sense. (They tried it once, at the dead of night in a motel room back in Roswell. Dana supposes they were trying to make love, but they both ended up sweaty and unfulfilled, and from then on their lovemaking retreated back to intimate glances and fond intonations.)
Their love was never wild passion and scorching touches. It didn’t ignite with a sudden spark and burn brightly with the scorching flames of desire. It was slow; a steady, calming thing like the gentle rocking of a boat in a quiet sea, anchored firmly in a bed of intimate friendship.
So it isn’t really that they break up – it’s more that they drift apart. Or maybe Mulder is the one who drifts and it’s simply that Dana has nothing left to hold on to. She’s been cast adrift before but it’s different now. Back then, she couldn’t speak to him because she thought he was dead; now she doesn’t speak to him because he never speaks back. She sleeps beside him at night, the two of them curled up together in the middle of their bed, but he’s never before felt so far away.
It’s Dana who can’t take it, in the end. She leaves him because she feels lonely, and she misses her best friend even when he’s sitting next to her. She leaves him because their house is too quiet, and there’s nothing to do except think and hope and wish. She leaves him because, in the oppressive silence, she finds herself yearning for the life they might have had, the son they might have raised. She leaves him and she doesn’t think she will ever stop feeling guilty for it, because she loves him and he needs her, perhaps now more than ever.
She leaves, but it doesn’t feel like they’re breaking up; it’s more that she drifts alone, out to sea, and Mulder – for the first time – drifts in the opposite direction.