“Prodigal Son” starts with Reverend Holt in the middle of a church service. He explains that Khalil is in the hospital fighting the battle of his life.
In the hospital, Jefferson, Lynn, and Jennifer arrive with Khalil’s mom and they’re all distraught at his condition. Moments later, Khalil wakes and asks for Jefferson’s help. He asks for Black Lightning to kill Tobias. When Jefferson refuses to kill Tobias, Khalil offers to give him all of the intel involving Tobias’ trade routes and business opportunities but Jefferson refuses to take it, saying the system needs to work his job.
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As she’s taking a walk in the parking lot, Jennifer’s looking at her hair in the reflection of a car. A white woman comes out and accuses of Jennifer of trying to steal it. The lady calls 911 saying an African-American is trying to break into her car and when the accuser isn’t looking, Jennifer uses her powers to strike the car with a bolt of lightning, causing it to explode.
Reverend Holt is continuing his sermon when he realizes something is on the cloth that he’s been wiping his brow with. He passes out and we see Cutter get up and leave the congregation.
Jefferson notices Jennifer is walking away with her hands on fire. He tracks her down and takes her to a secure location in an attempt to syphon off the fire using his electricity. Perenna arrives because she senses something is wrong and tries to calm Jennifer down. Perenna’s able to run through some mediation techniques with Jennifer and her flare up calms down.
Elsewhere, Lynn tries to convince Khalil’s doctors to try some experimental ASA methods on his treatment. One of the doctor’s is sure to mention that whoever built Khalil’s spine has out-of-this-world technology.
Inspector Henderson arrives to tell Jefferson that Holt had a heart attack in the middle of his sermon. Jefferson reminds Henderson that Tobias has been wanting to buy Holt’s clinic. Jefferson reveals that he knows where Tobias lives. Henderson refuses to hear the information unless Jefferson plans to help him out.
Jefferson and Henderson take a visit to Gambi’s shop, where Jefferson shows Henderson the tech setup they have in the basement. Downstairs, Henderson finds out that Gambi isn’t dead after all. Gambi reveals that he ran a toxicity screen on Holt’s body, saying the pastor has been poisoned.
After seeing what they have to work with, Henderson agrees to help the two take down Tobias.
Jennifer returns inside and reveals to her mother that she can look into living people and view their electrical synapses. She tells her mother she thinks Khalil is dying, but her mom advises her not to use her powers to help out. Jennifer then mentions that they should put Khalil in one of the pods at the ASA until they’re able to find out what to do.
Anissa’s waiting in the hospital’s waiting room when Grace brings her hamburgers and a drink. The two chat.
Lynn arrives with agents from the ASA and provides the doctor with a note from Khalil’s mother saying they have rights to run tests on Khalil. The doctor puts up a fight at first but after Lynn threatens legal action, they’re let in to run tests to see if Khalil’s compatible with a pod.
Henderson arrives at Tobias’ house to question him about the attack on Khalil. We see that Henderson is wearing a bug on his tie, allowing Jefferson and Gambi to get footage of Tobias’ apartment. Henderson’s able to get footage of Tobias’ safe for Gambi to analyze.
At prison, Tobias’ worker Todd bribes a guard for access to Dr. Jace. He deactivates her ankle device so that she can leave with him. He’s able to use new technology so that a hologram of her reading remains in her cell. Dr. Jace arrives at Tobias’ apartment, where she reveals that she’s the one who developed the anti-aging serum she and Tobias have both taken.
After running the tests, Lynn informs Jennifer that the ASA is unable to save Khalil in a pod because he’s not compatible. Jefferson warns his daughter to go say anything she needs to before it’s too late. Using Perenna’s powers, Jennifer and Khalil are able to enter her mind and go to prom and the two begin dancing.
Before long, Khalil starts coding and he passes away with his mother and the entire Pierce family at his side.