The story picks off where Part I left off, with the church collapsing a little with Connor still inside. Did you really think writers will kill off Connor? Frank Powell digs Connor out of pile and they need to think of a way to get to Miles and his patients before the church completely collapses. At this point, it will take some heavy machine to get all this pile of debris out of the way. That is going to take up a lot of time and the church may completely collapse by then. The insurrectionist leader says he know another way inside the church and leads Connor and Frank to a cave that connects to the basement of the church.
Back at the hospital, Dr. Durant finds that the disease is indeed bacterial meningitis. Dr. Kate Ewing immediately calls back to the United States to sent for vaccines. Eva continues to find the parents of the little boy.
As Connor and the team goes through the cave, they find the wall they need to crack open to get to the other side, where Miles and the others are. As they start cracking, the church shaken. Time is running out.
The pregnant woman Dr. Durant brought in from the clinic is now in need of an emergency C-Section. She and Ewing haven't done C-Section in a while. Nevertheless, they both perform the emergency and is successful. The baby came out alive, but is in critical condition. As more patients floods in, vaccines are not. Most of them were "robbed" by the local government. Ewing heads to the airport, trying to get those people to make sure the vaccines are going to the hospital. But a $50,000 offer was putted on the table in order to get the job done. Ewing turns the guy down.
Meanwhile, the parents of the little boy were found…dead. Eva now has to somehow get the bad news to the boy. The boy becomes upset as he receives the news that his parents didn't survive. Eva decides to file the boy for adoption, in hopes that he will find another family. However, the boy's big cousin shows up to pick up the little boy and Eva feels happy for him.
Connor digs Miles and the patients out. They escape the collapsing church just in time. However, Miles is infected with the disease. Connor convinces the father that the only way the boy can survive is to get them south to the hospital. However, he knows that the southern government wouldn't let them go if they catch the northern people. Connor promises to hide them in the hospital and the father agrees.
Connor and Frank arrive back at the hospital with the patients. When Ewing tells him that they don't have enough vaccines because the local government took them, Connor takes Frank with him in hope of recovering the vaccines.
While sneaking in the local government, Frank and Connor spot the truck with the vaccines. As security catches them trying to turn on the truck, Frank jumpstart the truck on time and they escape.
Back at the hospital, vaccines are disrupted to anyone who is infected. Connor and Frank take a couple of package back to the north, where Eva discovered that most infected people come from. When the insurrectionist father asks him about the boys, Connor says they will be all right. Connor decides to phone his son that he will be taking a long vacation to spend time with him. Then back at the hospital, Connor finds out that the two boys were taken by the local government army when they are scouting the hospital. Ewing tells him that she did her best trying to keep them, but came up empty. Connor becomes upset since he knows that the boy's father may never be able to see their sons again.
But the relieve effort is not over, the NIH continues to stay to treat the infected patients.
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