Billy stops gaping at a sparring match between Rivai and Sarah and calls them to watch, as the remaining ninjas shoot off the lock on the back of the truck. One ninja climbs aboard and unfurls a ramp, allowing the others to drive aboard. KITT charges up his EMP, but Mike insists on taking control, which doesn't go over well with Torres. Rivai orders Mike to zap the truck and wait for the incoming FBI team.
Knowing that the truck will jackknife unless he gets its speed under 80 mph, Mike pulls in front of the rig. With a rebel yell, he spins KITT 180, forcing the truck to slow down. The impact causes the ninjas in the back to drop their quarry, a vial of glowing liquid. The pulsating metallic virus immediately begins to engulf anything electronic or metal, searing the ninjas into their metallic body armor.
As the EMP forces the truck to a halt, the virus engulfs the driver. Rivai warns Mike not to approach the truck, but he pretends his earwig is jammed. A lone ninja rides off the back of the truck on what Mike recognizes as a '79 Harley Shovelhead - no electronics, so the EMP must not have had an effect. Mike peers into the back of the truck, shocked to behold a smoldering, infectious pile of metal.
Mike and KITT race back to the SSC, where they undergo decontamination. Mike tutors KITT on what it means to be partners: partners look out for each other. Torres lays into Mike, insisting that the EMP was set too high - that's what killed the ninjas. Graiman confronts Torres. The ninjas were killed by the Arrow virus, a nanovirus which attacks technology the same way an organic virus attacks humans.
The Arrow virus spreads through metal. If the Harley is a carrier, it could destroy everything in a 500-mile radius in a matter of hours, and if the virus uploads itself to phone lines, global disaster will result. Mike finds Sarah in a daze. She's already figured out that the Arrow virus killed the men, and they begin calculating the Harley's possible escape routes, figuring it will eventually stop for gas.
When KITT calculates a likely escape route, Mike hits the gas, telling Billy to monitor all gas stations in a 300-mile radius. Graiman enters the SSC to watch the Harley ninja visit a gas station, where the virus gets to work, mutating through AI and getting stronger. Since the virus doesn't affect humans, KITT is the one at risk. Graiman has him put up his shields on the approach, and KITT advises Mike to take off his watch and earwig.
KITT uses his laser to immolate an infected pay phone. With the virus contained, Mike and KITT take off in pursuit of the Harley. Back at the SSC, Sarah and Graiman confer. They both know that the virus originates with Graiman's former assistant and Sarah's former boyfriend, Ryan Arrow, who sold it to the Defense Department five years ago.
Having located the Harley ninja, KITT follows him down an access road to open ground, dotted by high-tension power lines. The virus jumps to the lines. KITT has to take down his shield and risk infection to access his plasma torpedoes to prevent the virus from spreading. Meanwhile, Graiman and Sarah find Arrow at his old hangout, a bar called The Well. Ryan is a more than a little smarmy, and obviously still carries a torch for Sarah.
Mike is concerned when Sarah won't respond, and is even more concerned to learn that she's at a bar with Ryan. He asks KITT to pull up a bio; even though Mike would like to think that Ryan's a geek, his profile makes him out to be a hot genius. Sarah asks Ryan for help with the nanovirus, but he maintains that he has no play since he sold it to the military - certainly, they're the ones who screwed it up.
When KITT reveals that Sarah's heart rate is elevated, Mike speeds to the bar. Sarah has started a bar fight, taking out a guy who called her "girlie," along with his pals. Meanwhile, the virus lurks around KITT's wheel well - he's a host!
Ryan takes Graiman, Sarah and Mike to his remote compound in the woods. Ryan claims that his original virus was harmless, designed to eliminate toxic waste. The military turned it into something else. Ryan maintains that Mike doesn't get it, since he's not a scientist. Regardless, Ryan has no idea how to stop the virus. Even if he did, he doesn't want to; the Army should dig themselves out of their own mess.
Back at the SSC, Rivai discovers that Ryan is still on the DOD payroll, and tells Billy to get Mike on a chatline. Mike goes outside to take the call, and immediately asks KITT to pull up blueprints on Ryan's house. KITT detects an impenetrable lead-lined room under the house with entry from a trap door on the deck. As the virus attacks KITT's chassis unseen, Mike confronts Ryan: why did he let the virus go?
Mike roughs up Ryan, who chides him for being a jarhead. Mike explains that he's Army all the way, and he works for himself - Ryan is still on the government payroll. Shocked, Sarah demands to know what's going on. Ryan takes everyone into the lab and admits that when the DOD approached him to buy the virus, he caved to seven figures. When he found out they were transporting it, he tried to steal it back, thinking it was his one chance to put the genie back in the bottle.
Unable to reach Mike and Sarah in the lab, Torres orders KITT to scan the house. Glowing with the undetected virus, KITT concludes that the house is empty. Thinking that Ryan means to spread the virus through his Internet connection, Rivai advises Torres to obliterate the compound and let the virus burn itself out.
Back on the deck, Mike overhears KITT arming his missiles, and orders him to abort. Realizing his mistake, Torres orders KITT to abort the attack, as Mike yells for everyone to run. Ryan insists on going back into the lab for an anti-virus, and is killed when his house explodes. Back at the SSC, Torres and Rivai struggle to figure out what happened. Zoe suggests that KITT is infected with the virus, but Billy claims he's clean.
On the ride back to the SSC, Mike asks KITT if he's sure he doesn't have the virus. KITT claims his scans are clean, and he doesn't know what malfunctioned, but he is feeling regret for causing a wrongful death. Mike explains that only humans have feelings, but KITT knows he's feeling something. When they pause in the tunnel for decontamination, the virus jumps off KITT into a wall vent.
Graiman wants to decommission KITT until they figure out what's wrong. After all, KITT is hardwired not to harm humans. When Torres picks up the phone to inform Washington, the virus leaps out of the receiver. Torres drops the phone and runs to initiate full quarantine - they're infected! When Billy fails to disconnect from the Internet, Zoe grabs an axe and starts chopping wires. On a hunch, Mike loads Sarah into KITT and drives off - otherwise KITT will die.
As the virus uses AI to spread quickly through the SSC, Sarah explains that KITT's carbon fiber delayed his infection. Struggling to gain control of KITT, Mike and Sarah start singing to distract him. Billy estimates 15 minutes before they lose total control, so Rivai recommends full evacuation, and starts the two-man self-destruct sequence with Torres. Hoping to kill the virus by self-destructing the SSC, Graiman and Torres prepare to go down with the ship, and order Billy and Rivai to leave.
Mike drives KITT back to Ryan's house, where a barn containing the Harley still stands. The Harley is armed with a computer that's running an anti-virus. Mike asks Sarah if she can synthesize an antidote for KITT. She struggles to find the password, which Mike knows can only be "Sarah." Sarah rushes to download the antidote and plug it into KITT's dashboard. When it works, she has KITT upload it to the SSC.
With seconds to go, Graiman finally hears Sarah calling to abort the self-destruct. Rivai rushes in at the last minute to initiate the two-man abort sequence with Torres, and the SSC is saved with one second to go. On the way home, Mike asks Sarah if KITT can experience emotion, but she thinks it's probably an anomaly caused by the virus. Apologizing for Ryan's death, Mike takes Sarah's hand. Everything's gonna be alright.