Disclaimer: I don't own Skinner or Scully or Mulder or baby or mother. Or a house with a widow's walk.
A/N: Time is fluid. Also, I haven't yet seen Season 8; I just know what happens. This is my prediction of Scully's emotional process: details might be off. Please let me know if something's really horrifically wrong.
When he was taken, all pretense fell away quite abruptly.
There was no more "We're just partners," or "He's my friend." There was no hedging, no avoiding, no evading. And everyone knew it.
Suddenly, everyone was treating her like a widow. Not like an agent who'd lost a partner, not like a woman who'd lost a friend. Like a widow. And she didn't even have the energy to fight it, because she was grieving like a widow. She was grieving with the knowledge that she'd just lost the greater part of her life, that she'd loved him more than she could even love herself, that he'd irrevocably changed her, that part of her was gone. And what energy she can gather is fully channeled into searching for him, into trying to reassemble the shattered pieces of her world.
She remembers hearing about ships lost at sea, and wives waiting and watching for their sailor-men to return, hoping with everything they had and yet knowing better. She's seen the widow's walks on the roofs of old New England houses, and she grimly wonders how high she'd have to be to see him coming home. She doesn't even know where to look.
And then he's returned, and the pit in her stomach is gone, but the ache in her heart intensifies, because she truly is a widow. Female agents give her pitying glances in the hall, men look away from her, Skinner's secretary Kim who's been there through all the years lays a hand on her shoulder in silent comfort. Her own mother, also a widow, does her best to make her Dana understand: when you're a widow, everyone assumes your life is in pieces, is gone, and it is but it isn't, and no one really knows how to talk to a zombie. You're a Scully, Dana, and you can fight; you'll be fine.
And so she plays the widow for those around her, and perhaps, a little, for herself.
And then he is alive, and he is her second miracle this year, and she doesn't know whether to thank God or to fear Him, because she can't decide if she's the Virgin Mary or Mary Magdalene, or even what that means. She decides it doesn't matter.
She also decides that she's played the widow for too long to back down now. She doesn't care what Skinner thinks, she doesn't care what anyone thinks, she doesn't care what Mulder thinks. She loves him, dammit, and that's important. And it's not worth pretending she doesn't anymore, not when she's carrying a child that is probably his, not when she's watched him die, not when she's spent months grieving him.
The pretense is gone, and she kisses Mulder by the light of day, because life is too impossible not to.
Note: I'm sorry if anyone is bothered by the Mary Magdalene comment. As a Catholic, I find her part very interesting. However, whether or not you believe she was married to Jesus, she did love him. Many people did. And he loved her back. He loved everyone. And that's what I based that comment on: mutual and unconditional and miraculous love.