DISCLAIMER: Star Trek and everything affiliated with it belongs to Gene Roddenberry, JJ Abrams, and all of the other awesome people who own it. All I own is the plot…
The story comes out one night after Bones has received a private call in his office. He tells Christine to cover the rest of the shift—they are a day away from their next planet, and it has been two days since their last shore leave, so there should not be any problems—and leaves.
Christine calls Jim, who goes to Bones' room once his shift is over and finds him sitting at the kitchen table. The lights are so dim that just about all he can see is the glint of fluorescent lights on Bones' glass as he lifts it to take a sip of what Jim guesses is either bourbon or whiskey. Probably whiskey.
"Bones?" He says, entering the room hesitantly.
Bones grunts and kicks a chair out for Jim to sit down, pushing another glass toward him.
Jim sits and picks up the glass, but doesn't drink. "What happened, Bones? Chapel said you left in a hurry."
Bones is quiet for a long time, but there is something in his eyes that Jim can see even in the dim light of the room. It keeps Jim from repeating the question. "I can remember the exact moment when I knew Jocelyn didn't love me, anymore."
Jim wants to say something, but he can't find the words.
"I was in Iowa already, about a week before the shuttle left." Bones continues. "And she calls me up and says…that she's caught something incurable."
Jim drinks. He hasn't caught as many STDs as people think, but he knows which ones still aren't treatable even today and that he's damn lucky he's somehow managed to avoid them.
"Then she says she wants to get back together." Bones says, and laughs bitterly. "And then she says, 'You know, Leonard, we won't even have to use protection anymore, once you've caught it.'" He sounds like he's going to cry. "And it finally hit me that she doesn't give two shits about me."
"…Bones, I…" Jim tries to speak, but can't. So he just reaches across the table and grabs Bones' hand.
"I'm over it, now." Bones says, and knocks back the rest of his glass. After he swallows, he lets out that laugh again that sends a shiver up Jim's back. "Or, at least, I thought I was."
"Bones, what happened?"
"I got a call from a friend of hers." Bones says. "One of the friends we shared before everything went to shit and people chose sides. One of the friends that chose her side. Although most of 'em did, in the end."
Jim wants to tell him to just fucking say it already, but he thinks Bones needs this. Needs to say it at his own pace.
"She got an abortion." The glass drops out of Bones' hand, which moves up to cover his face. "Right before the divorce. She didn't even tell me she was pregnant."
"Oh, God." Jim says. He can only imagine how Bones feels, and the way Bones' shoulders shake make him think his imagination doesn't know the half of it.
"And when that friend asked her why she didn't at least tell me, first, she said she 'didn't need another snot-nosed brat hanging around and making Leonard want to try again.'" Bones lets out a sob that makes Jim start crying, too. "I knew she hated me, but Jesus Christ."
"Shit, Bones." Jim says, standing and then kneeling at his friend's side. He puts his arms around Bones and asks, "What do you want me to do? Just name it, Bones, and it's done."
Bones shakes his head, returning Jim's embrace.
Jim assumes that this means Bones needs a quiet shoulder, so he provides it even though it goes against his nature to be quiet for any length of time. When Bones pulls away and goes to bed, he follows, even though Bones has started retreating into his grumpy doctor mask and claims to want him to go away.
A few days later, he grabs Bones at the end of the shift and takes him to an airlock. In it is a small hamster ball that Scotty had bought for his tribble and Jim had…confiscated, then sealed up the holes. Inside it is a lit candle, and there is a flash of understanding in Bones' eyes as Jim opens the air lock and the ball flies out into space. Then Jim grabs Bones' hand, bows his head, and starts praying for Bones' lost child.
Bones puts his head on Jim's shoulder and watches until the light is snuffed.