Spoiler Alert – This special episode recaps the first 12 episodes. If you have not yet listened to the first 12, you may wish to start with Episode 1.
Simon Dougherty is a cyber offensive specialist working for the NSA. He’s also a diabetic, receiving treatment from Dr Clement Garvin at a nearby medical facility. When an attack on the facility by the terrorist group KANTO leaves him injured, he discovers his life has been a lie. Instead of bone and blood, he finds his body is composed of metal and electronics. He confronts Dr Garvin, who had to have known this. Simon senses, however, that Garvin now means to destroy him. He murders Garvin and goes on the run with his girlfriend, Gretchen Williams, in tow. Their destination? MIT and the man who taught Simon so much: Dr Hadoop.
On their way to Cambridge, Simon and Gretchen stop in Rhode Island to visit Simon’s mother and to get some answers. Instead, they find a woman suffering from mental instability. Simon’s special senses kick in, alerting him to danger. They flee the house just as Mrs Dougherty blows the house up, killing her. As helicopters rush onto the scene, Simon and Gretchen again flee.
Arriving in Cambridge, Simon and Gretchen meet with Dr Hadoop, a specialist in Artificial Intelligence. Simon reveals his nature, leaving the good doctor in disbelief. This technology goes far beyond what mankind is capable of. The sudden trigger of a fire alarm forces the three to seek cover. Hadoop leads them to a top secret lab in which he’s developing some kind of satellite for the government. They tap into some security cameras to reveal a team armed with microwave weapons is searching for them. Once the threat has passed, Hadoop takes them to see a friend who may be able to shine more light on Simon’s nature.
That evening, they arrive at the back door of Dr Natalia Warkovsky, director of biological and computational learning. Despite friction between her and Gretchen, they learn the cyborg technology may be alien and that the neural network that integrates Simon’s organic brain with his android body is likely responsible for his heightened senses and ability to detect danger and even read people’s emotional states. The entire group is captured when Simon’s boss, Mr Kazin, arrives with a team of NSA field agents.
Back at the NSA, Director of Tailored Access Operations, Ms Aster, listens in on a recording retrieved from Simon. It is clear that Simon has been used to infiltrate the Agency and exfiltrate data to KANTO. Meanwhile, Chet, a forensics expert, tries to determine exactly how Simon is put together. Before he can get very far, however, an armed Gretchen breaks into the forensics room and rescues Simon. As they flee Fort Meade, she reveals she is actually a KANTO operative and she was rescued as she was being brought in. She uses a device to disable Simon’s body and they flee south.
With Simon’s nature revealed and his escape at the hands of KANTO, Mr Conway, a senior leader within IAD (Information Assurance Directorate) grills Kazin over his failure to capture Simon. Kazin is granted the opportunity to redeem himself and go after the cyborg. Chet is brought before Director Aster and reveals what he learned from Simon before he escaped – that he may have been designed by aliens. Ms Aster instructs special agent Roger Boyle to go after Simon, suggesting that there may be some within the agency with a hidden agenda. Mr Conway, the sponsor of Hadoop’s satellite project meets with the doctor and offers additional resources to ensure the project is completed on time.
Agents Boyle and Abrahms begin trying to find Simon, starting with Valerie, Dr Garvin’s admin and the last person known to have seen Simon. She provides them with the name of another doctor who worked on Simon’s case – Dr Bannister. Drs Hadoop and Warkovsky take the Acela train back to Boston and discuss their situation and the idea that alien technology could be involved. Feeling ill, Dr Warkovsky excuses herself and goes into the restroom. A few seconds later, a gunshot is heard. Dr Warkovsky killed herself.
Boyle and Abrahms turn their attentions toward Dr Bannister. They arrange a meeting over the phone, giving Abrahms a chance to exploit the doctor’s smartphone and spy on her calls. They discover her connection to KANTO when she calls Gretchen seeking orders. They use the information gained to follow her to KANTO, where Simon is held captive. They drive south through Hurricane Norris.
When Dr Banister arrives at the KANTO lair, she is taken to meet the leader of the terrorist cell, a man named Marius. They question Simon about Boyle, and he lies, saying that Boyle is a manager of Disaster Recovery at the NSA, and no field agent. They decide to risk the storm and move their operations inland. Mr Kazin and his sidekick, Agent Brown, have been tracking Boyle and Abrahms and are also aware of the KANTO lair’s location. When Boyle’s car get stuck in the mud, they take advantage of the situation to place a tracker on the KANTO vehicles.
As they head inland, Marius explains to Gretchen the details of the cyborg project – how the technology was stolen from the Chinese, how it was given to them by aliens, and how Simon’s father had once volunteered to become a cyborg, but the technological flaws in the design forced them to kill him. They worry those same flaws may be present in Simon. Kazin and Brown identify an ambush site and prepare to capture Simon and take out the rest of the KANTO operatives. They order a fake roadblock and call in helicopters to attack them. Simon, however, breaks out of the cage he was transported in and, using newly discovered abilities of his neural network, triggers an electrical failure in the helicopters, causing them to explode. He and Gretchen escape the wreckage and flee into the woods.
Kazin comes upon the failed ambush to discover a badly wounded Marius, who he takes into custody. He reports in to Conway who, despite being very angry at the failure, grants Kazin one more chance to capture Simon. He takes a team of agents into the woods to track them, sending Marius back to DC for further interrogation.
Boyle realizes Kazin and Conway are not true to the Agency and he decides they need to rescue Marius and let Simon take care of himself. Simon and Gretchen eventually hide out in a cave in the mountains. He senses Kazin closing in, however, and they make a break for it. The hunters have them surrounded, however, and are waiting for them. Simon gives them the slip, though, and attacks, killing both Brown and Kazin. It is in killing Kazin that they discover his secret – he isn’t human. Kazin is an alien.