Elizabeth discovered her pregnancy in "Mr. Gregory Devry". She was assaulted by a man who accused her of being a traitor. Keen was taken to the hospital, where the doctor informed her that although she had broken some ribs, the baby was fine. In "The Vehm", Liz created a list of pros and cons of keeping the baby, which Tom discovered after she left for work. Afterwards, she would have informed Red, but he already knew, having noticed because of her humor and habits.
Lately, as Liz constantly wonders about giving her child up for adoption, Tom makes it clear that he wants it, and Red himself tells her about her own mother, Katarina Rostova, whose pregnancy was also unplanned but ended up seeing the child, Liz, as a blessing. Finally, she realized that she had been right when she considered that her life would always be full of violence, partially due to Red's presence, and called an adoption agency.
Elizabeth made an agreement with the agency so they would ensure that her baby would be adopted by a couple willing to take an open adoption, which means that she would be able to be in touch with the baby. In "Alistair Pitt", however, she's informed that the couple rejected the open adoption due to Liz's case with the attorney general.
When Liz finally finds a couple willing to take an open adoption, however, she externalizes to Red how difficult she thinks it might get. In the last minutes of "Lady Ambrosia", Liz is seen reading to the child in her womb.
Months probably have passed in the following episode, "Drexel", where the pregnancy looks more evident. In the final minutes, Liz watches a recording of Tom at the adoption agency, telling that he thinks Liz would be a good mother, and she feels the baby kicking. Then, she goes to the hospital and tells Tom that she wants to keep the child.
Tom and Liz decided to get married once again, and the wedding ceremony takes place at a small church in D. C. In "Mr. Solomon: Conclusion", however, Tom and Liz needed to escape from his ambush at the church, and, while they do it, the car crashes and they make their way to a hospital, where Liz goes into labour.