The leader of the Autobots, Optimus Prime, came to Earth shortly after Bumblebee sent his comrades a beacon. Upon atmospheric reentry, Prime managed to land outside of Tranquility's inhabited areas. While Sam and Mikaela watched, Optimus transformed and left his landing place. From atop a hill, he quickly scanned the form of an Earth truck, thus configuring his body to transform into it. Prime, Jazz, Ratchet, and Ironhide met up with Bumblebee and his human friends, Sam Witwicky and Mikaela Banes in an alley. In one of the most extended transformations in the multiverse, Prime assumed his robotic form before the stunned humans. After confirming Sam's identity, Prime introduced himself and his team. When Mikaela asked of the Autobots' intentions, Prime explained the search for the AllSpark, the betrayal of Megatron, and why Sam was important to their search.
Optimus Prime will watch you fornicate. And there is nothing you can do about it.
Glasses that belonged to Sam's ancestor, Captain Archibald Witwicky, contained the location of the AllSpark encoded across its lenses, so Optimus Prime ordered his troops to wait outside Sam's house while Sam and Mikaela searched inside for the glasses. Much to Sam's exasperation, Optimus Prime, in his impatience, clumsily ruined his parents' garden, and the Autobots' heavy footsteps convinced them there was an earthquake. Prime's attempts to hide, such as having the Autobots transform into vehicle mode right in the backyard, were also less than satisfactory. Ultimately, Sam came so close to a panic attack that Prime was forced to order the Autobots to fall back. As Prime lectured his team on their supposed inability to remain quiet, Ratchet got himself shocked by walking into some powerlines, causing further problems. When the parents came to investigate, Prime's attempt to avoid discovery caused the house to shake, though this was to their benefit, as the father assumed that the damage to the yard was the result of an earthquake. Ironhide suggested that they kill the parents, but Optimus scolded his old friend. Despite all this, their presence remained undetected until Sector Seven arrived (in a convoy of GMC Yukons) and abducted Sam, Mikaela, and Sam's parents.
Optimus Prime sent the Autobots in pursuit of the SUV that contained Sam, Mikaela, and Sector Seven's director, Agent Simmons. Prime intercepted the vehicle carrying their young human friends, ripping the roof of the vehicle off, with the other Autobots disarming the agents, and made it perfectly clear to Simmons how pissed off he was at him for trying to apprehend the two children, regarding this as a bad move on Simmons' behalf. Optimus then ordered his comrades to relieve the agents of their weapons, and attempted to interrogate Simmons. The agents' lack of surprise at their appearance indicated that they had seen Cybertronians before, but Simmons refused to reveal any information. With a Sector Seven backup team en route, Prime ordered the Autobots to scatter, while he took Sam and Mikaela. While hiding under a bridge, Mikaela and Sam slipped and fell off Prime's shoulder. Bumblebee managed to catch them before impact, but was captured, and Sam and Mikaela recaptured, by the organization after their retreat. Now in possession of the glasses which could tell him the location of the AllSpark, Optimus regretfully left Bumblebee in Sector Seven's hands, knowing that if they went after him, they would have to use deadly force.
After regrouping the next day, Prime used the glasses to locate the AllSpark. Jazz again raised objections to leaving Bumblebee behind, but Prime remained firm in his belief of not harming the humans. Ironhide seemed okay with using deadly force, stating the humans were too violent, but Prime countered that when their time had come, the Cybertronians had been little different. Going on to explain the potential he saw in the humans, as well as reminding them that "freedom is the right of all sentient beings", Prime revealed to the Autobots his real plan for the AllSpark: if they could not defeat the Decepticons, Prime intended to merge the Cube with his spark. Though this would destroy the AllSpark, Ratchet cautioned Prime against this, as it would also kill him. Prime believed that this was acceptable, vowing not to let another race suffer the mistakes of the Transformers. The glasses placed the AllSpark at Hoover Dam where, luckily, Bumblebee and the young humans were taken.
Optimus Prime's team met up with Sector Seven, Bumblebee, Sam, and Mikaela en route, who had planned to hide the AllSpark in nearby Mission City. While on the highway, he was attacked by Bonecrusher, who managed to tackle Optimus and drag him over the edge of a freeway overpass. During the battle, Optimus struck the rage-filled Transformer so hard his optic popped out. As the Decepticon swung his claw wildly, Optimus drew his sword from his right arm and sliced off one of Bonecrusher's arms, before brutally finishing off his enemy by driving the blade through Bonecrusher's neck, severing his head.
Optimus arrived at Mission City just in time to observe Megatron discarding the remains of Jazz, and challenged him. Millennia in the ice had done nothing to lessen Megatron's hatred of his brother, and he launched himself in jet mode at the Autobot leader. Optimus leaped and grabbed hold of the wings, which was a really bad idea, as Megatron drove himself and Prime through an office block. As they flew out of the building onto the street below, Megatron transformed and leapt on top of Prime, declaring the humans undeserving of life. Prime rejected his claims, saying that they deserved to choose for themselves. Megatron threw Prime across the street, declaring that if he wished to defend the humans, Prime could die with them. He then formed his fusion cannon from his forearms. The power up time allowed Prime to draw his ion blaster and fire, hitting Megatron. The Decepticon used the momentum to spin around, then used the fusion cannon to blast Prime across the street into another building. Megatron then resumed the hunt for Sam and the AllSpark.
Tracking Megatron to the deserted building, Prime barely managed to catch Sam after Megatron knocked him off the roof. Telling the boy to hold onto the Cube, Prime attempted to scale down the building, but Megatron jumped on Prime, causing them both to fall down hard onto the street below. Sam survived, however, and Optimus told the boy that if he could not defeat Megatron, Sam must put the AllSpark into his chest which would destroy it. As Sam sought cover, Optimus faced down Megatron, and informed him that, "At the end of this day, one shall stand, one shall fall". Unfortunately, Megatron, even after years of stasis, proved to be far too powerful for Prime to defeat alone. The unit led by Lennox and the Raptor squadron laid down suppressing fire as Megatron reached for the AllSpark, until Optimus finally took him down by sweeping his legs. Still, Megatron continued, crawling toward the cube. Believing he had lost, Optimus implored Sam to put the AllSpark into his chest. Sam instead thrust it into Megatron's chest, killing the Decepticon leader and destroying the AllSpark.
As Optimus watched his brother die, he regretfully said there was little other choice. He also told Sam he owed him a debt of gratitude for saving his life, but was then informed that Jazz had not survived (Jazz was flapping around disrespectfully like a ragdoll during this sequence). Prime briefly eulogized his comrade, then commented that they had gained new comrades in the humans, and was honored by their bravery. Bumblebee, who had finally regained his voice, requested permission to remain with Sam Witwicky, to which the young human eagerly agreed, and Optimus approved. He noticed a fragment of the AllSpark in Megatron's chest cavity and removed it, then permitted the humans to dispose of the Decepticon corpses by dumping them into the deepest part of the ocean.
Though Megatron was killed and his Decepticons were defeated, the AllSpark was destroyed, leaving the Autobots unable to restore Cybertron. The Autobots elected to remain on Earth, and Prime sent a message into deep space to any surviving Autobots in the Galaxy to come to their new home on Earth, their long years of searching having finally having come to an end. As the other Autobots rested (and watched Sam and Mikaela make out on Bumblebee's hood) Optimus Prime looked to the sky, hoping his message had been heard.
After the events in Mission City two years ago, Optimus Prime and the Autobots became part of a Transformer/human military group called NEST, which hunted down the remaining Decepticons across the world. When Demolishor and Sideways were detected in Shanghai, NEST was deployed there, including the Autobots Sideswipe, Ironhide, Arcee, Skids and Mudflap. Once Demolishor made himself known by transforming into robot mode and crushing dozens of cars along the highway, Sergeant Epps radioed an overhead C-17 to release the Autobot leader. Optimus Prime parachuted out of a NEST cargo plane and landed in vehicle mode. He leapt off a bridge onto the Decepticon's head as he plowed through it. When the massive Constructicon refused his order to pull over, Optimus unleashed several blasts of his ion blaster into Demolishor's head. These shots, coupled with Ironhide destroying his tires, sent the titan crashing to the ground and into a warehouse. As he and Ironhide approached the dying Decepticon, Optimus asked if he had any last words. With his dying breath, the Constructicon stated that The Fallen would rise again. Optimus responded in the negative and unceremoniously executed him.
Returning to Diego Garcia, Prime entered a briefing with Theodore Galloway, the National Security Adviser who had been appointed liaison by the President, and General Morshower, the Chairman of the Joint Chiefs of Staff, who was watching by satellite feed. Prime relayed the warning of The Fallen to them, but Galloway made no effort to conceal his hostility toward the Autobots. He noted that while they had given them intelligence and the sole remaining AllSpark fragment, Galloway took issue with their refusal to share weapons technology and their continued sending of transmissions into space. Prime told Galloway that the Autobots were aware of humanity's history of warfare, and Morshower said that all the transmissions had been vetted by NEST officers. Galloway also pointed out that despite Megatron's death and burial in the Laurentian Abyss and the destruction of the AllSpark, the Decepticons had not left Earth as Optimus had hoped, leading him to conclude that the Autobots were the ones who the Decepticons were after. When asked if the Autobots would leave Earth peacefully if told to, Optimus replied that they would honor their request, but warned Galloway to consider what would happen if the Autobots left but the Decepticons did not.
Unknown to Prime, the Decepticon Soundwave had been monitoring transmissions and spied on the briefing. Dispatching Ravage to the island, he had his agent steal the remaining AllSpark fragment, killing several soldiers in the process. The incident left the Autobots with rather chilly relations with the United States. Seeking outside help, Optimus dispatched Bumblebee to retrieve Sam Witwicky from college in an effort to secure his testimony on the Autobots' behalf. Meeting Sam at an abandoned cemetery near his college, Optimus explained the situation. Sam was not receptive; in fact, he was quite hostile, saying that he had just started college and was trying to have a normal life. Knowing that fate often called at inconvenient times, Optimus impressed upon Sam the importance of what was going on, but Sam reiterated that the Cybertronian War was not his, and that they didn't need him. Optimus relayed his fear that it soon would be, and silently said that they needed him more than he realized.
Prime's fear soon came to pass, but in the last way he could imagine: the Decepticons had used the AllSpark shard to resurrect Megatron, who had learned that the knowledge of the AllSpark had been passed to Sam by a fragment Sam had touched, and soon captured him, Mikaela, and Sam's college roommate Leo Spitz. Heading to rescue the three humans, Optimus and Bumblebee ambushed the Decepticons in the abandoned industrial complex where the teens were being held, just as Scalpel was about to perform fatal neurosurgery on Sam. Knocking Megatron and Starscream out of the building, Optimus managed to whisk Sam away from the plant. Optimus made it as far as the nearby forest when Megatron arrived. Going one-on-one with the Decepticon leader, Prime managed to hold his own, all the while trash-talking Megatron. Megatron then called for Starscream and Grindor, who quickly arrived. Prime was forced to run interference between Megatron and Starscream, who pursued Sam.
As the battle raged, Megatron told Prime that the boy was the key to finding another energon source, then shattered his mouthplate and sent him flying back with a point blank shot from his fusion cannon. Megatron asked if the boy's life was greater than the future of their race, but Prime knew that he would never stop with a single life. Declaring that he'd take them all on, Optimus Prime unsheathed his Dual Energon Swords and fought a three-on-one fight against the Decepticons. Surprisingly, not only did he manage to hold his own, he was actually winning, managing to stab Megatron multiple times, slice off Starscream's arm and use it as a club, and rip apart Grindor's head. However, Megatron managed to stab his own sword through Optimus Prime's chest, following with a point blank shot through his injured back. Critically injured, Optimus implored the still-observing Sam to run. Although the rest of the Autobots soon arrived and drove off Megatron and Starscream, Optimus Prime was dead.
Soon after, The Fallen made his presence known and demanded Sam Witwicky be turned over to him or the world would be destroyed. Galloway used this as a reason to shut down NEST and ordered the Autobots returned to Diego Garcia under guard, along with Prime's corpse (which Galloway callously denounced as a piece of scrap metal). Fortunately, Bumblebee, and the Twins managed to spirit Sam, Mikaela, and Leo away before The Fallen made his announcement. With help from their former enemy Seymour Simmons and the Decepticon-turned-Autobot Wheelie, the group discovered that Sam's mind contained the Language of the Primes, to which group The Fallen had once belonged. The human/Autobot group managed to locate the Seeker Jetfire, who told them of how the Dynasty of Primes forged a star harvester to use a star's energy to replenish the AllSpark, and the Matrix of Leadership, needed to activate the harvester, until they were betrayed by The Fallen, who tried to harvest Sol in defiance of the Primes' rule of the sanctity of life. Sam hit upon the idea to use the Matrix to restore Optimus to life, similar to how the Decepticons had used the AllSpark fragment to resurrect Megatron. Having been teleported to Egypt by Jetfire, the group managed to relay the information to Major Lennox and Sergeant Epps, who faked engine trouble over Petra, where the Tomb of the Primes was located. Unfortunately, the Matrix had turned to dust in the thousands of years since its entombment, but Sam still believed that it could be used to revive Optimus.
However, the Decepticons were still looking for the harvester and the Matrix needed to activate it. Sam was technically killed in the battle, during which he communed with the six Primes from the tomb, who restored the Matrix. Jamming it in the fallen Autobot's chest, Sam used the Matrix to restore Optimus Prime to life. Unfortunately, The Fallen soon arrived and stole the Matrix. Having been fatally injured by Scorponok, Jetfire offered his parts to Optimus, as only a Prime could defeat The Fallen, and snuffed out his own spark. After Ratchet and Jolt finished attaching Jetfire's wings and thrusters to Prime's body, Optimus hurried to the Great Pyramid of Giza, which had been constructed around the harvester, and damaged the machine before it could destroy Earth's sun.
Optimus Prime then faced Megatron and the Fallen. This against the odds battle went far better for Optimus, as he used Megatron's own fusion cannon to shoot off half his face and his afterburners to send him through some ruins. Optimus then battled the Fallen, using his Energon Sword to slice through his face. The Fallen countered by ripping off his left wing and striking him with it, but Optimus managed to grab the Fallen's own spear and impale him with it. Telling the traitorous Prime he had picked the wrong planet, Optimus used the spear to rip off The Fallen's face plate. As The Fallen tried to flee, Optimus Prime punched through his abdomen and crushed his spark core, killing The Fallen and forcing Megatron and Starscream to retreat.
On the return voyage home, Optimus thanked Sam for saving his life, as the boy thanked the Autobot leader for believing in him. Following this, Optimus Prime sent another transmission into space, detailing recent events so that the pasts of both races would be remembered, and also declaring that Humanity and the Autobots would face the future
Three years after the battle in Egypt, Optimus arrived with human NEST operatives in Chernobyl to investigate a report about the presence of Cybertronian technology on site. However, this investigation was interrupted by Shockwave and his tamed Driller, attempting to steal the component. After driving them off and cutting one of the Driller's tentacles off, Optimus examined the piece of technology and, to his disbelief, identified it as a fuel cell from the Ark. Optimus returned to NEST headquarters and refused to transform or speak to anyone until National Intelligence Director Charlotte Mearing arrived. He demanded an explanation from her, which she offered along with the corroborating testimony from Buzz Aldrin that the information had been known by a select few. Optimus explained that the Ark carried important technology that would have been to used to win the Cybertronian Civil War, and was piloted by his predecessor and mentor, Sentinel Prime. Optimus mounted an expedition to the Moon aboard the Xantium with Ratchet to explore what was left of the Ark.
The two Autobots explored the ship and opened the crash vault in which Sentinel Prime had locked himself. Optimus pulled Sentinel from the vault and brought his former mentor back to Earth where he used the Matrix of Leadership to revive Sentinel. The former Prime awoke and attacked in confusion. After calming his mentor down, Optimus explained that they recovered five pieces of his technology, but Sentinel was disturbed by this news, explaining that purpose of the "pillars" was to form a space bridge. Optimus declared their peaceful uses to the humans, but Director Mearing objected, citing possible uses like transporting weapons and troops to the planet. The pillars were placed in human custody.
After this meeting, Optimus took Sentinel for a tour on the countryside at sunset, during which Sentinel commented on the peaceful beauty of Earth. Optimus bowed and offered the Matrix of Leadership to him, declaring him the rightful Autobot leader. Sentinel refused, saying that while he was Optimus's master on Cybertron, here on Earth, Optimus was the more experienced of the two. After learning from Sam that the Decepticons were targeting Sentinel because he alone could control the pillars, the Autobots were ordered to protect him. Running behind the group, Optimus returned to the NEST base only to find that Sentinel had betrayed the Autobots and NEST, killed Ironhide, and escaped with the pillars. Mearing declared the subterfuge and defeat as the fault of the Autobot leader. Optimus voiced no defense at this accusation.
Optimus subsequently tracked his mentor to the National Mall reflecting pool and attempted to stop him from bringing an invasion force to Earth. Sentinel fought and bested Optimus but spared his life, commenting that Optimus would come around to his way of thinking. Prime refused to be part of Sentinel's plan. Later, Sentinel denounced Prime and his Autobots as rebels, and demanded that human beings exile them. Fearing an attack from at least 200 hidden and entrenched Decepticon troops, human leaders ordered the Autobots off the planet. Prime complied with the order and gathered his troops to leave Earth immediately in the Xantium. Despite Sam's pleadings to reveal his plan to fight back (and inform the Decepticons who had bugged him), Optimus replied they had no plan. He reminded Sam that the human was his friend and the fight against the Decepticons would now be his own. Shortly after takeoff, Starscream attacked and destroyed the ship. Optimus and the Autobots were presumed dead.
However, the Autobots had hid themselves in one of the disengaged boosters and survived, thanks to the Xantium's builders, the Wreckers. Optimus and the other Autobots headed for Decepticon-controlled Chicago and arrived there just in time to rescue Sam, Epps, and a team of former NEST soldiers from a Decepticon fighter. Optimus explained that the Decepticons would never leave Earth in peace, and that Earth's leaders needed to believe they had gone so that they could see the truth. As the other Autobots arrived on-scene, Optimus announced that they were going to take the battle to the Decepticons in the name of freedom.
On route to Sentinel's location and that of the master pillar, Optimus and the Autobots were ambushed from below by Shockwave and his Driller. The Driller disengaged Optimus's trailer, but the Wreckers distracted the Decepticon assassin. Optimus managed to recover the flight tech from his trailer and attack the Driller from the air just as it bared down on Sam, Carly Spencer, Epps and his soldiers. Optimus swooped through a building and punched a fatal blow through the Driller. Shockwave, angered by the destruction of his pet, shot at Optimus from the street. Optimus fell through a nearby unfinished building and was caught up in the wires of a construction crane. While the Wreckers tried to get him loose, Sentinel engaged the pillars and started to transport Cybertron into Earth's orbit. The Wreckers managed to free their leader, who swooped into the main battlefield and killed eleven Decepticons single-handed. Charging toward Shockwave, who had already been damaged by NEST soldiers, Optimus then ran his spiked fist through his side and tore out his eye. He then used his enemy's cannon to blast the control pillar, temporarily stalling the transportation of Cybertron.
Optimus demanded his former master to come down and confront him. Sentinel complied, but when Optimus started to get the upper hand, Sentinel called upon Decepticon fighters to fire at his former pupil. Pinned down by the enemy fire, Optimus was prevented from attacking until the fighters were destroyed. Optimus engaged Sentinel again, but this time he cut off Optimus's right arm. As Sentinel prepared to deliver the final blow, Megatron charged up, shot Sentinel in the back and proceeded to heavily damage the older Prime. Megatron then proposed a truce to Optimus on the condition that he would be in charge again, saying, "who would you be without me Prime?" Optimus replied that it was "Time to find out." He swung his axe into Megatron's head and ripped it out, taking Megatron's head and spine with it.
The damaged and helpless Sentinel explained that Optimus had to see why he had betrayed his own side, for their race's survival in the long run. Optimus refused and told Sentinel he had betrayed himself. Despite his former master's plea for mercy, Optimus fired two shots from Megatron's fusion shotgun, executing Sentinel. With Cybertron now (presumably) destroyed, Prime, Bumblebee, Ratchet, Dino, Sideswipe, and the Wreckers finally accepted Earth as their new home, and Optimus declared that the Autobots would never forsake the defense of Earth or its people.