The Matthew's baby boy is still in the hospital and the doctor reveals that he has a respiratory infection that will keep him there for a while longer. Alan and Amy stay by their newborn, which they decide to name Joshua Gabriel Matthews, and pray for him to overcome his illness. Cory is having a difficult time accepting the fact that his brother may not make it home from the hospital, and he turns to Topanga for support. Cory wants Topanga take his hand and tell him that everything is going to be ok, but instead she tries to get him to face the reality of what is happening. Topanga tells Cory that they aren't little kids anymore, and she can't defuse such a serious situation by simply holding his hand. She talks to Angela about how Cory is ignoring reality and not dealing with his feelings. Angela tells Topanga that without her, all Cory has is reality, and he needs her to be there for him in anyway she can.
In the meantime, Eric spends time with his new buddy Tommy; a young orphan who looks up to Eric like a brother. Tommy learns about Eric's baby brother and wants to go visit him in the hospital. After they return to the apartment, Eric finishes packing his things. Although he isn't sure where he going to live, Eric doesn't want to interfere with Jack and Rachel's new relationship, and he thinks it is best to move out.
Back at the hospital, morale seems to be low until Shawn shows up, returning from his soul-searching road trip. With Shawn there, it helps everyone, especially Cory, take their minds off the possible negative outcome of little Joshua. Instead, Cory and Shawn are optimistic in talking about all the good things to come, like Mr. Feeny having another Matthews to teach. There's good news all around when the doctors finally let Amy and Alan take the baby home.
Before they leave Alan says a prayer for all the babies that will ever have to be in the position that Joshua was in, and Topanga and Cory resolve their disagreement by apologizing to each other.