Prowl, Jazz, Optimus and Sentinel Prime were searching Detroit for rogue Decepticons, when Sentinel mysteriously disappeared. Optimus spotted an unknown robot with a strange helmet, but when he followed he found Sentinel with the "Sunstorm" Starscream clone in stasis cuffs.
The took the captured Decepticon back to the Elite Guard ship, and when the clone was placed in the brig, much to Optimus' surprise, Sentinel had Blitzwing and Swindle detained as well.
When questioned, Sentinel was enigmatic about how he captured all of these Decepticons all by himself. Prowl and Optimus surmised that he was hiding something. Optimus mentioned seeing the robot in the helmet, so Prowl browsed through their database until Optimus identified the helmet. Prowl was shocked when Optimus identified the helmet of Yoketron, Prowl's old martial arts teacher, who was thought to be dead.
Prowl remembered how he first met Yoketron. Prowl had been hauled in by Warpath, as a draft dodger who refused to fight against the Decepticons. Yoketron offered to keep Prowl out of prison, if Prowl would allow himself to be trained in martial arts.
Prowl sped off and told Jazz, a fellow student of Yoketron, of his discovery. Jazz and Prowl decided to follow Sentinel Prime on his next patrol to discover the connection between Yoketron, Sentinel Prime, and the ease at which Sentinel was capturing Decepticons. Though they trailed him closely, he suddenly disappeared again.
Prowl remembered his training with Yoketron, and how Yoketron taught him that the warrior is more powerful than his tools.
He and Jazz gave up their search for Sentinel and returned to the Elite Guard ship, where they discovered Jetfire and Jetstorm working on the ship's Interspace Guidance Gyro-stabilizer. Jetfire informed them that Sentinel Prime wished to see them in the brig, where he had Lugnut detained. When asked how he captured this Decepticon, he gave another detail-less answer, after which he sent the twins to continue working on the Subspace Guidance Gyro Stabilizer, since their spare is missing.
Prowl noticed that the Decepticons were all missing their weapon modifications, and accused Sentinel of working with Lockdown, the bounty hunter who worked for upgrades. Sentinel disputed Prowl's analysis when he showed him Lugnut's explosive punch modification locked away in storage. Sentinel explained that he disarmed the Decepticons after capture.
Prowl reminisced back to his training with Yoketron, when he was first presented with his shuriken. he also remembered being taken into the Cyber-Ninja Corps hall of honor. Prowl noticed that one pedestal was empty. Yoketron explained that was once the spot of a student who brought shame to the Corps. He then showed Prowl their true duty: to guard a secret cache of Protoforms, who would be used against the Decepticons if Project Omega failed. Yoketron told Prowl that if he could master the Processor-Over-Matter technique he could be the greatest Cyber-Ninja. Prowl failed in his first attempt, so Yoketron sent Prowl on an "Optics Quest", so that Prowl could "find his spark" and fulfill his potential.
After his flashback, Prowl (disguised by a hologram as a cabinet) overheard Sentinel talking to his secret accomplice over his internal radio. Prowl, once again, followed Sentinel, while Jazz went for backup. This time he was led to Tigatron Stadium, where he found the Ramjet clone captured by Lockdown (who was wearing Yoketron's helmet). Sentinel offered the missing Gyro-stabilizer to Lockdown in exchange for the captive clone. When confronted by Prowl, Sentinel justified himself by stating that he was actually capturing Decepticons. The Ramjet clone further illustrated this by declaring how helpless he was because he was disarmed. Prowl tried to warn Sentinel that the clone was a pathological liar, but it was too late. The clone attacked Sentinel just as Lockdown revealed that the Decepticon made him a better offer.
Lockdown and Prowl squared off and Lockdown revealed that he was the student who had fallen from grace. Prowl recalled when he found a helmet-less Yoketron dying and most of the Protoforms stolen. Prowl tried to save Yoketron by placing his master's spark into a Protoform, but Yoketron died anyway, telling Prowl not to sacrifice a piece of the future for the past.
This memory spurred Prowl to defeat Lockdown and reclaim his master's helmet. Optimus and Jazz arrived to help Sentinel against the Ramjet-clone of Starscream, just as Prowl took the helmet from Lockdown. The helmet was booby-trapped, and wrapped Prowl in crushing metal bands that immobilized him. Lockdown took Prowl into his ship, so that the bounty hunter could steal his personal modifications. In Lockdown's ship, Prowl saw that Lockdown had replaced the battle armor that Prowl had borrowed and destroyed when he and Lockdown as previously worked together. Prowl then began to use the Processor-Over-Matter technique to free himself from his bonds, while Lockdown was preparing his tools.
Outside, Jazz and Optimus fought to free Sentinel Prime, but his Decepticon captor kept using Sentinel as a living shield. Optimus finally blinded the Decepticon with flame-retardant foam, which forced him to drop Sentinel Prime.
Meanwhile, Prowl surreptitiously escaped his bonds and donned the battle armor, including Yoketron's helmet. Lockdown turned and was surprised to see the Autobot Ninja free and ready to fight. Prowl knocked Lockdown out of the airlock, and the two continued to battle in the stadium.
Safeguard (the combined form of Jetfire and Jetstorm) knocked the Ramjet-clone out of the sky, so that Optimus could drop the scoreboard on it. Prowl and Lockdown fought into the path of the falling structure, and as it collapsed, Optimus feared for his comrade.
Prowl survived unscathed by using Processor-Over-Matter to levitate the pieces that would have fallen on him. The Ramjet-clone was captured, but Lockdown escaped.
Back in the Elite Guard ship, Optimus re-established communications with Cybertron. Cliffjumper informed them of Shockwave's revelation and his attack on Ultra Magnus (who is recovering from his wounds). He told Cliffjumper that all of the Decepticon prisoners were captured by Prowl, much to Sentinel Prime's dismay.
Later, in Prowl's quarters, Jazz complimented Prowl on the new armor, and that Yoketron would be proud to have Prowl wear his helmet. Prowl swore to do all that he could to be worthy of it.