Alone again, Emily throws herself into her studies. She reconnects with Nikolas, who was now a single father to his and Courtney's son, Spencer Cassadine, following Courtney's death. They bonded while taking care of Spencer. When Spencer was kidnapped by Helena, Emily helped Nikolas rescue him by briefly letting Helena take her hostage. Spencer was rescued, and Nikolas named Emily as Spencer's godmother. The two decide to rekindle their romance, but are caught in a hostage crisis at the Metro Court Hotel. Jerry Jacks, going by the name of Mr. Craig, holds the two and several of their friends hostage with a bomb in order to get a package in the hotel's security vault. When Elizabeth goes into premature labor and her father Alan has a heart attack, Emily is forced to choose which one would be released. With Elizabeth's urging, Alan is released, but his heart attack proves fatal. Jerry goes on to inject Nikolas with a poison requiring a daily antidote. Elizabeth, Robin, and Patrick Drake help Emily develop an antidote that saves Nikolas' life.