I always felt that this is a song about a girl who got pregnant and married way too young to a man who spends most of his time outside of the house. She has no chance to make a life on her own as she has no life experience to set her own path and will now have to raise this child more or less alone. This terrifies her. She's trapped in the home provided to her by her husband but she know's he is unfaithful ("while papas far away making up children's stories" is a reference to this man having multiple children with multiple women). "Two babies in the dark" is a reference to both her and her unborn child. She's scared both internally (as she is so young and helpless she cant even help herself, even less this child she's bringing into the world) and externally in the fact that she is alone, in a dark home, alone and that anything could happen to her and she wont be able to stop it and no one will come to her aid.

the only solace she can possibly find, is a promise to care for the child ("ill put you to sleep at night....sing you lullabies...teach you about everything"). However (and this is fantastic as a final line of the song as its very loud, almost a cry when the band sings it) she asks that the baby "please save me". the line is sung very desperately as to suggest that she knows how unreasonable, unfair and dangerous it is to expect the unborn child to provide any kind of strength or stability.

This song is about the working class family in modern America. Stuck in a crappy house or apartment in a bad part of town, while a mother is terrified to be alone in the house and a father spends all his time working to put food on the table and struggling to make a life for his family. He spends his time making up children's stories while never getting to see his own family, because he works too hard. Meanwhile the mother doesn't feel safe at home alone. It's a commentary on the irony of a father who makes up children's stories for a living while never seeing his own family, while his wife is terrified by every strange noise in the house.

The last part would me for either his wife and child or two children; I think it means for them to be there for him. In other words being his support.

The 2 babies in the dark are referring to both the unborn child in the womb and the mother. They are waiting, trying not to be afraid while the father's far away and they really have no knowledge of his condition (" ...far away making up children's stories" supports the idea that he's at war). The unborn child inside the mother knows as well, and just as much as the mother, fears the consequences of papa being at war ("the little one's inside, so afraid to be alone...") and the mother is trying to be brave while she's alone. The last verse is written from the perspective of the father begging to come home. Safe...

Alright this song is about alien abductions, more specifically the effect that the phenomenon has no abductees. The lyrics have many reference s to abductions which, if you read a lot of the books about it, become clear. For example, Why you hide underneath the cover hiding from the abductors. There's a baby in your womb a reference to implants and pregnancies induced by the aliens. The song is about people who claim to have been abducted are not lying, they believe that they have been/were/are being abducted. Victims of alien abductions need help. That is either protection from their captors, or psychological help. And society, governments etc just laugh at them mock them and make them feel stupid/crazy. This is taken even further by the line while papa's far away making up children's stories. Implying that a girl is being abducted and impregnated by the aliens (hence two babies in the dark, referencing to her and her unborn child) and her father won't believe her. Or perhaps Brett was talking about the government cover-ups, in that her father works for the government and its is job to cover up alien abductions (make them children's stories).
So the song is saying, regardless of whether aliens really do abduct people, the abductees need help not ridicule.

My interpretation of the song, a few lines at a time.
"There's a light on in the hallway, so I can't understand, / Why you hide underneath the covers. / There's a baby in your womb, so don't be scared tonight, / Because Raggedy Ann is in the closet picking posies." - This verse sort of sets the tone for the rest of the song; an empty house, a light on in the hallway, but with nobody in the other room. There's a baby on the way, so nothing could ever harm you.

"Two babies in the dark, like diamonds in the sand, / While papa's far away making up children's stories / The little one's inside, so afraid to be alone, / She's trying to be brave until the daddy comes home" - The chorus, to me, shows what this song's really about; there's two babies in the dark, sitting home alone in the dark, while papa, the soldier, is far away. He's making the history that'll be a children's story someday, while the kids are at home. So afraid of being alone, but being a brave little girl for her daddy. Putting it in historical context(The Gulf War), I think it's about all those little boys and girls whose fathers went off into the Middle East, and what they felt while they were away, with some of them never to come back.

"So if you chance to see her, please tell her it's alright, / Cause everyone fights the tendency to snap. / Sometimes it's not a matter of being brave and strong, / 'Cause noises in the house are terrifying." - This part is, I think, a little reassurance that the father wishes he could send home. Comforting words, saying that everything's all right, it's ok to be frightened, etc.

"I'll put you to sleep at night, like a foreign movie. / I'll sing you lullabies, and I'll teach you about everything. / And I'll only ask one thing, please save me." - I'm not sure how this fits in with the rest of the song, but they sum up to this; I'll help you sleep, I'll teach you whatever you want to know, I'll sing to you at night, I'll read you stories, anything; just save me in return. Maybe it means 'I'll do anything, just get me home?'