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Fauxlivia was given a death sentence if she chose to keep her baby. The VPE virus that killed her sister was present in her, as well, and the odds of one or both surviving a deliver with the virus are astronomical. She chooses to terminate.
Walternate has Fauxlivia kidnapped and her pregnancy accellerated in order to do something we are not yet privy to.
Lincoln and Charlie go on a wild search for her, meeting Henry along the way. He brings the switching of the Olivias to their attention and Lincoln goes to Walternate for answers.
Walternate acts kind and concerned as he tells half truths to Lincoln to keep his own plans hidden, but gives enough information for Lincoln and Charlie to successfully locate Fauxlivia and the baby.
Lincoln declares his love for Fauxlivia as she gives birth, nearly dying. Both she and the baby miraculously survive.
Walternate is, of course, behind the events of the entire evening and we are left, again, wondering just what kind of man he is.