Alien: Special Agent Dana Scully has gone through hell and back for her job. In past seasons she had all her eggs harvested and a tracking device implanted in her sinuses that gave her cancer when it was removed. She's also been shanghaied and placed inside a pod on an alien ship. No doubt an alien embryo could have been implanted inside her somewhere along the line, and only now is it beginning to mature.
Chances: 25%

Fox Mulder: At the end of season seven, there was a scene that ended in Scully's bedroom. Executive producer/creator Chris Carter has been teasing fans over the past couple of months with the notion that Mulder and Scully may have actually done the nasty at that time. For the leagues of loyal X-philes who have watched the show from the very beginning, this would be an extremely cheap shot. Seven seasons of foreplay and we don't get to witness the deed? Lame. To add some fuel to this fire, Scully's also been having dreams or visions of the imprisoned Mulder being poked and prodded on the alien ship.
Chances: 20%

Clone Implant: It seems like Scully ends up in the hospital at least every other episode. This would have given the evil government conspirators ample time to clone an embryo and place it inside of Scully. Additionally, clones have played a major part in the ongoing X-Files saga. The next logical question is: Whose clone is it? As we've stated, Scully is getting vibes about Mulder, so perhaps the fetus is somehow tied to her partner's consciousness.
Chances: 15%

Gibson Praise: Sex with a minor is a felony in most states, so once again we're looking at an implanted fetus. Young Gibson is already an alien hybrid, but if you add Scully's DNA and brainpower you have an uber alien-human crossbreed.
Chances: 10%

Cigarette Smoking Man: This bastard has been resurrected at least a half-dozen times. At the conclusion of the last season, Krychek left him for dead after he pushed his wheelchair down the stairs. However, since we didn't see the funeral, we're willing to bet he rises from the ashes once again. However, CSM is getting up in years. He'll need a little Cigarette Smoking Baby to finish up his dirty work. Gross as it may be, CSM could have impregnated Agent Scully during one of her hospital stays.
Chances: 10%

Asst. Director Walter Skinner: Not only are they good friends and respected colleagues, but Skinner seems to have a certain affinity toward our dear Special Agent Scully. In fact, he's the only one who knows she's pregnant. However, unless Chris Carter plans to totally screw with X-Files mythology, this scenario borders on incest.
Chances: 10%

The Lone Gunmen: These guys haven't had a date since college -- if even then. Frohike has declared on more than one occasion that he thinks Scully is hot, but he probably wouldn't know what to do if the situation presented itself. Although they have studied all the possible conspiracies in which Rohypnol may have played a part, deep below their geek exterior, they're much too sweet to use it on Scully just to cop a feel.
Chances: 5%

Alex Krychek: We wouldn't put anything past the Rat-Boy: He's doublecrossed everyone so many times, he's practically in knots himself. He's probably still pissed off that he didn't have a part in the X-Files movie. However, in addition to the when and the where, the why with Krychek poses a bit of a problem in the conception department. Additionally, Krychek isn't scheduled to reappear on the show until late April.
Chances: 5%