Prowl is an experienced militia and police officer, who joined Optimus Prime's Autobots in the war against the Decepticons, contributing his knowledge of combat in urban areas. His weapon of choice is the Investigator Special—a electroconductive gel that's quite adept at redirecting internal signals, paralyzing his targets long enough for him to bring them in.
Prowl acted as go-between for the civilian High Council guards and various city-state militas. He allied with Optimus during Megatron's attack on Praxus. During the siege of Iacon, Prowl informed Optimus that Megatron was aboard Trypticon Station. Optimus feared Megatron had found a new weapon. Alpha Trion asked the Autobots what they knew about energon. Prowl tried to silence Jazz's jokes as he felt anything the Archivist had to say was significant, but even he laughed when Jazz felt Alpha Trion had not sufficiently explained what Energon was when he said it was the emanation of Primus. Alpha Trion then adequately explained Megatron had found Dark Energon, the emanation of Unicron. Optimus ordered Prowl to lead a guerilla team to draw out the Darkened Decepticons, to waste the resource in chases, when Prowl received a communication from Starscream requesting a meeting. Prowl offered to go meet him in case it was a trap, but Optimus requested Starscream speak to him on a secure channel instead. When the Darkened Decepticons stole the Plasma Energy Chamber, Prowl helped fight them off and got Ratchet to repair Omega Supreme, whom Megatron almost killed. Afterwards, Prowl received a distress signal from Sentinel Prime. He traced it to Kaon, as he recognized the signal blocking its source was used by gladiators to hide messages they didn't want on the Communication Grid from his pre-war days working in the Hydrax-Badlands circuit. Prowl rescued Sentinel with Optimus and Jazz. While recovering, Optimus went to Cybertron's core to purge its Dark Energon corruption and returned declaring Project Generation One. Prowl became part of the Eight Track crew, boarding Trypticon and sustaining heavy damage battling its drones and Minicons. He helped destroy its Dark Energon Facility, causing it to crash into the planet. He boarded the Ark with the other Autobots, journeying through the last space bridge to a spiral galaxy. Then Prowl detected the AllSpark.
After passing through the unstable Space Bridge, Prowl and the Autobots aboard the Ark found themselves in the vicinity of a Cybertronian colony world called Velocitron. They located it in part thanks to a mysterious starmap projected outwards from Optimus Prime's chest by the Matrix itself. Prowl was assigned to Hound's second response team, as Optimus Prime made planetfall with his initial squad. It was a time of great stress between Velocitron's rulers, Override and Ransack, and the Autobots' arrival from mythical Cybertron only exacerbated the situation. Worse still, Prowl uncovered evidence of a Decepticon agent on Velocitron. He overheard a secret meeting between a mysterious robot called "777" and several Velocitronians, spreading Megatron's message of "Peace through tyranny". Prowl was unable to get a good fix on 777's face or voice, but after active sabotage temporarily disabled the Ark, he came to the conclusion that one of their crew was actually a Decepticon agent. Jazz and Prowl conferred with Optimus about the situation, but ultimately concluded there was little they could do at the moment other than remain on guard. Although the Autobots secured an ally in Override, they left Velocitron on the brink of civil war during their departure, as Ransack's followers had been corrupted by the Decepticon rhetoric spread by the Ark's traitor. The next leg of their journey through the Space Bridge brought the Autobots to fabled Junkion, a world composed entirely of space junk. Prowl was on board the Ark during the initial landing again, and was therefore present when the engines blew out in another act of deliberate sabotage. At Prime's request, he kept an optic on the shifty Junkion named Axer, whom even Junkion Leader Wreck-Gar didn't trust. Prowl got some intel on Axer from another Junkion named Shearbolt, and learned that not all Junkions were natives—some came from Cybertron and other worlds, and Axer was among the most recent arrivals. Shearbolt seemed to be holding something back, and so Prowl resolved to keep both him and Axer under observation during their time on Junkion. Unfortunately, Shearbolt disappeared soon afterwards. And when Prowl eventually located the Autobot—dead and stuffed inside a starship belonging to Axer—Ratchet confirmed via energon decay that Shearbolt had been dead BEFORE Prowl supposedly had a conversation with him. Shocking as it was, this confirmed the existence of a mythical "Shifter", one of the descendents of the Thirteen's trickster, Amalgamous Prime. Tracking down Axer, he confirmed that the Autobot they thought was Hound was actually a Decepticon shifter named Makeshift. After securing Makeshift, Prowl and Ironhide oversaw the repair work on the Ark while Optimus Prime finished up his Matrix-driven quest on the other side of Junkion's Space Bridge. Makeshift's Decepticon comrades found them, however, forcing Prowl and the others to square off against the Seekers while waiting for Prime to return. He eventually did, and the situation became a bit too esoteric for Prowl's taste...multiformed legendary figures and weapons out of myth threatening to tear apart the planet. The situation resolved itself once Prime got a heading for the AllSpark in a flash of insight. Unfortunately, Megatron shared that insight, and the two Cybertronian forces began a race to acquire the prize.
When the Matrix led the Autobots to a planet called Aquatron, Prowl led a recon unit down to the planet including Kup, Rodimus, and Bumblebee. They established a beach-head on the northern continent and made contact with the seemingly friendly Curator, governor of the Aquatronians. Once Optimus Prime and the others landed, however, Optimus suffered a mysterious seizure requiring him to be treated by the Aquatronians, making many of the Autobots suspicious of their hosts. Soon after, the Aquatronians revealed their true nature as agents of the Quintessons when the Decepticons arrived. The Aquatronians disabled the Ark and the Nemesis in orbit before politely insisting that the Autobots and Decepticons engage in peace talks, with the Curator as moderator. Optimus skeptically agreed.
Indeed, the "peace talks" were a sham from the beginning, orchestrated by the Curator to fail and bring the Cybertronians before a kangaroo court of trumped up charges before executing them to harvest their energon for an invasion of Cybertron itself. When Optimus and Megatron were separated from the others during a single combat exercise, Jazz and Prowl led the Autobots in escaping from their cells to strike back against the Quintessons' Sharkticon guards. Alongside the Decepticons, they fought a holding action at Hydratron while Optimus and Megatron dealt with their true foes. Afterwards, the Autobots and Decepticons coordinated a joint effort to locate their missing leaders among the wreckage, and found Optimus Prime and Megatron side-by-side atop a friendly Leviacon.