WARNING: Spoilers
The synopsis contains information that may give away important plot points. You may not want to read any further if you've not already seen this title.
After defeating Sentinel Prime and Megatron's army in Chicago, the Autobots have gone into hiding after the government deemed all transformers as threats, and thus, began to hunt them all down. The government has thus replaced the Autobots with their own transformers using technology from the fallen transformers. Meanwhile, a mechanic, his daughter, and his daughter's boyfriend become dragged into the conflict upon discovering Optimus Prime in their possession, and all the while, a mysterious new enemy, Lockdown, sets his eyes on earth.
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In the three years since the Battle of Chicago, the Transformers have become outlaws. At the behest of CIA Agent Harold Attinger (Kelsey Grammer), a major campaign has been brought about to hunt down and destroy and and all Autobots or Decepticons that are still active.
Unknown to several different parties, Attinger is also working with an intergalactic bounty hunter named Lockdown (Mark Ryan). Working with a mercenary team known as The Cemetery Wind (led by James Savoy (Titus Welliver)), the group manages to find the Autobot Ratchet hiding in Mexico. After wounding the former Autobot medical officer, Lockdown demands to know where Optimus Prime is. When Ratchet refuses to tell, Lockdown rips Ratchet's 'spark' from his chest, and hands it over to Savoy and his team.
Meanwhile, in Paris, Texas, inventor Cade Yeager (Mark Wahlberg) and his partner Lucas Flannery (T.J. Miller) investigate an old movie theater for mechanical pieces they can probably salvage. While going through the dilapidated auditorium, Cade is amazed to find a flat-nosed semi truck hidden amongst the debris. Stranger still, the former theater's owner has no recollection of how it got there!
Cade purchases several of the theater's mechanical pieces intending to refurbish them, and the semi rig, intending to strip it down for parts. Needless to say, his daughter Tessa (Nicola Peltz) does not find his latest endeavor as anything more than her father shirking his responsibilities (their home is in danger of foreclosure, and Cade has been siphoning power from a neighbor). Cade still contends that his inventions and intentions will yield results, and help pay the way for Tessa to go to college.
While going over the semi-truck, Cade is surprised to find that the insides of the truck still activate, even though various mechanisms should have been damaged given its damaged state. When Cade hooks up a battery to the engine, and hears a booming voice say "Calling all Autobots," the inventor is sure he's found a Transformer!
Lucas claims that if they report the truck to the government, they could make $25-100,000 off of the find, which Tessa also backs up as a good idea (given that the money will pay off their debts, and give them some money she can use for going to college). However, Cade refuses, and instead wants to restore the truck, and investigate what makes it tick, confident that its alien technology can help him make his own creations work.
As he attempts to fix up the truck, it violently transforms before them all, into Optimus Prime (Peter Cullen). Optimus at first thinks that Cade and the others are there to hurt him, but Cade assures Optimus that he just wants to help. Optimus then tells how he was ambushed, and sent a message to the rest of his Autobot colleagues to hide, as an unknown party wants to hunt them down.
Things heat up when someone reports Cade's purchase of the semi truck, and soon, the Cemetary Wind are dispatched to Cade's property, where Savoy threatens to kill Tessa unless Cade gives them Optimus. Hearing Cade and his family is in danger, Optimus blows his cover, attempting to buy his human comrades some time to escape. In the firefight, Cade manages to grab a small drone that the Cemetary Wind guys are using.
Luckily, Tessa' (secret) boyfriend Shane Dyson (Jack Reynor) just happened to be coming by in his Rally Racer, and they pile in as Savoy and his men give chase. Optimus himself takes off, but is soon accousted by a grey Lamborghini, which is Lockdown! Both battles collide in the ruins of an old factory, where Shane's rally-racing skills help them take off most of the Cemetary Wind's crew. However, when the axle breaks, the group runs for it, but not before Lockdown unleashes a flash-metal weapon, that catches Lucas, encasing him in metal, as Cade, Tessa, and Shane jump into Optimus and drive away.
Optimus takes the humans to a dilapidated Gas Station, and drives off for bit, to make sure they haven't been followed. At the station, Cade is incensed that his daughter was seeing a boy behind his back (as he had forbid her to date anyone), though Shane and Tessa insist that they have known each other since high school. When Cade mentions Lucas' Irish accent, the young man mentions that he came to the states to Rally Race (and currently has Red Bull as a sponsor). However, given that his means of racing has been wrecked, he is willing to stick with Cade and Tessa, though mainly to take care of his girlfriend.
After the spat, Cade manages to use some technology in the old station, and hacks into the mini-drone he grabbed during the firefight. He is able to view the imagery it has recorded, including images that show the destruction of Autobots Ratchet, and Leadfoot, by the Cemetary Wind crew.
When Optimus Prime returns the next day, the group heads west towards Monument Valley, but not before stopping off at a small ATM. Using the drone, Cade attempts to have it use his ATM card, only to find that certain parties have locked his account. Needless to say, the transaction attempt is found out by Attinger, and a group of police cars quickly descend on the location looking for Cade, but the group is long gone.
As they near Monument Valley, Optimus scans a passing long-nose semi truck, and his exterior turns into a flashier, more modern semi rig, complete with red flames on a blue body. Pulling up into Monument Valley, several other Autobots emerge from hiding: Hound (John Goodman), Drift (Ken Watanabe), Crosshairs (John DiMaggio), and Bumblebee.
The other Autobots are wary of the humans Optimus has brought, but soften when their leader tells how they have helped him. Shortly afterwards, Cade shows the group the mini-drone's footage, and the other Autobots want to find out why they are being hunted. Cade also wishes to help them, to find out the people responsible for threatening his family.
Their investigation leads them to a company named KSI, located in Chicago, Illinois. KSI is headed by future-tech wunderkind Joshua Joyce (Stanley Tucci), who has been working with Chinese Entrepreneur Su Yueming (Bingbing Li) and Harold Attinger, to create man-made Transformers, to eventually be used for Military use.
Studying the remains of Megatron, Sentinel Prime, and numerous other pieces of alien hardware from after the Chicago war, the group has managed to synthesize a metal called "Transformium," which when given commands through a computer, can be manipulated into various shapes.
KSI has already made a drone based around Bumblebee's design, named Stinger, but Joyce's major project is an even bigger drone that he has named Galvatron. However, the attempts to make Galvatron to Joyce's standards has not worked, as all prototypes have been unable to form properly from the Transformium used, and the final robot design does not meet Joyce's request to make it resemble Optimus Prime.
With Bumblebee's help, Cade and Shane manage to have fake ID badges made, and Cade manages to infiltrate KSI. Using the mini-drone, Cade beams imagery back to the Autobots about what he is seeing, including a small Autobot named Brains (Reno Wilson), and the severed head of Ratchet, which is being melted down to obtain the Transformium material within him.
Unfortunately, the use of Cade's ID badge is found to be fake, and he is caught by security, and taken to see Attinger. Attinger tells Cade that what he has seen is a precaution, to make sure that the world will be safe, and demands to know where Optimus Prime is. However, Cade still refuses to talk.
The image of a fallen comrade's remains being mutilated sends Prime into a fury, and he leads the Autobots on a charge into KSI's facilities. Bee manages to rescue Cade from Attinger's office, and the group then breaks into the manufacturing floor, intending to destroy the works before Joshua Joyce appears. Joyce claims that what is being done is as a deterrent to any further Transformer damage, and claims that the humans "don't need" the Autobots anymore. The group does manage to free Brains from his captivity.
Optimus Prime then leads the others out of the factory, only for Attinger to then accost Joyce, claiming the Autobots have pretty much declared "open war" on the humans by breaking into the factory. Attinger is able to coerce Joyce into using Stinger and Galvatron to take down the Autobots. On a highway leading out of Chicago, the two human-controlled drones transform, and attempt to take down the Autobots.
Of the two, it is Galvatron who is sent after Optimus Prime, who attempts to stab Galvatron in his 'spark chamber,' but finds none. When Prime is surprised that his combatant doesn't have a spark, the human-made Transformer growls, "that is why I have no fear!"
Suddenly, a volley of shots knocks Optimus Prime to the ground, and Lockdown and his ship appear. As Galvatron then drives away, Lockdown glowers over Optimus Prime, telling him that his Creators "want him back." A net is then deployed, and Optimus Prime is hoisted up into Lockdown's ship, along with a nearby vehicle.
It happens that Tessa had sought refuge in the vehicle, and Cade attempts to get her out, but fails.
Lockdown then has Optimus Prime put in a cage, and Optimus Prime notes several other aliens in