Overview
Ever since it came out in 2014, Age of Extinction's explanation for what exactly took place between it and Dark of the Moon was never completely clear. This has prompted many to voice their own theories to at least provide an unofficial explanation, including a certain Theorymus video that was extremely thorough. In short, they were probably all wrong because they never managed to get around to the bigger picture, one involving a lot of politics and secret deals. Instead the focus was always on which Autobots got killed and whether or not Sam Witwicky died, though I can tell you right now with complete certainty that he didn't. Now go on and read the true recounting, discover for yourself how it all makes perfect sense and why it also wouldn't have made for a very entertaining film.
2013 A.D.
Directly following the Battle of Chicago, the primary objective of the United States is to find and obtain all alien technology left in the wreckage of the city before anyone else can get their hands on it, especially foreign nations. This becomes difficult, however, once President Barack Obama issues an executive order for the city of Chicago to be rebuilt as soon as possible, with civilians and foreign agents alike managing to make their way into the city disguised as private contractors to covertly extract alien technology. The nations that succeed the most in this are Japan, India, and Israel who managed to get their hands on a couple of ships. Within the United States, the black market is flooded with the tech, launching a CIA investigation into the identities of the distributors.
While all of this is going on, the Non-Biological Extraterrestrial Species Treaty has been brought back. The Autobots, led by Optimus Prime, work with the US Military to search for the remaining Decepticons hiding on Earth, mostly ones tasked with distributing the Pillars around the globe who weren't present for the Battle of Chicago. Progress in this objective is very slow, with few leads ever turning up as to the whereabouts of any Decepticons. Back at home in America the government, in preparation for the possibility that Decepticons are hiding within the country itself, establishes a phone number that citizens can call into to report alien activity under the toll-free 855 area code number. To rule out the possibility that citizens will try to handle things themselves in pursuit of personal gain, the state puts out an offer of a possible $25,000 reward for those who call in and have their reports confirmed.
This plan backfires, however, as citizens who were hoping that their fears of another Chicago war were going to be allayed are told directly by their own government that the threat isn't gone. Anti-Transformer sentiment becomes widespread, prompting the creation of several hate groups that put up posters suggesting that even the intentions guiding the Autobots don't pertain to the good of the American people and could very well be the opposite. A veteran intelligence operative within the CIA named Harold Attinger observes this and decides to take advantage of it, as he is of the ideology that the very presence of the Autobots in America invites another war. Attinger brings up the suggestion that N.E.S.T. be disbanded to all the high-ranking officials within the CIA, with a great deal of them agreeing that it’s the correct course of action. The one major roadblock Attinger finds in his way though is the director of the CIA, who shoots down the proposition and orders Attinger to go back to his job within the investigation of the alien weapons circulating the black market.
2016 A.D.
After two years of not having the authority to further his goals, Attinger gets hit with a stroke of luck. The CIA director retires and his replacement is much more receptive to Attinger’s proposition, going as far as to pull a few strings in order to convince some law-makers to draft up a piece of federal legislation that would abolish all joint-combat operations between the military and the Autobots. This bill doesn’t make it very far within the current administration before being vetoed by President Obama himself, but unfortunately, the election cycle has just started up. Only a year later a new presidential administration of the rival party has been instated, and out of awareness towards the escalation in civil unrest among the American populace, the bill is approved to pass into the Supreme Court for revision. This process is slowed, however, through the efforts of N.E.S.T. founder, Colonel William Lennox. He makes a strong case for the record of the Autobots in fighting alongside the military, stressing the point that they're still needed. Through this he manages to divide the court on the issue, driving a wrench into Attinger’s plan.
In the interim, the government decides to issue a special contract to a research and development company heavily invested in by China called Kinetic Solutions Incorporated (KSI) run by multi-millionaire, Joshua Joyce. This contract grants KSI access to a wide array of recovered alien technology, with their job being to reverse-engineer it. Upon analyzing the metal that the Transformers are made of, Joshua discovers that it's molecularly unstable and as such should not be capable of being used for any industrial purposes. Hoping to find out more about it though, Joshua hires a geologist and ex-girlfriend of his, Darcy Tyril, to go search for more of it. What's discovered is that the metal has only ever been found in trace amounts within Antarctica, prompting her to attempt to find out where deposits of it are most prevalent. While he waits for word back from Darcy, Joshua is approached by the man who got him the contract in the first place, Harold Attinger.
Hoping to have an early retirement, Attinger had approached Joshua with an offer that he get him the contract if he could get a 5-figure share in KSI, whose stock would inevitably skyrocket after the company gained access to the alien technology. Joshua told Attinger about the elemental metal, so Attinger had it in the back of his mind when he got a call from a Transformer who claimed to be unaffiliated in the Autobot and Decepticon war, Lockdown. He had loaned out his talents during the War for Cybertron as a bounty hunter, but soon after the war’s stalemate he took up a bounty from the Creators on the Knights, who had been labeled fugitives. After pursuing the bounty for centuries, Lockdown had managed to deliver every remaining knight back to the Creators, even being allowed to turn their ship he commandeered into his own personal prison. The final knight Lockdown needs to capture, is Optimus Prime.
2017 A.D.
Lockdown arrived on Earth aboard the Knight Ship, and having wished to be unhindered in his hunt, used the World Wide Web to find humans in positions of power who’d be willing to assist him. Through this he found Harold Attinger and offered to take the Prime off his hands free of charge in exchange for his help in accessing him, but Attinger made a counter offer, claiming he’d provide Lockdown with CIA assets in exchange for more of the metal that his race is made of. Lockdown happened to have collected a Seed as a trophy in his travels across the many galaxies and promised to give it to Attinger once he had the Prime is in his possession, but also promises to kill Attinger if he only ends up as a hindrance to his hunt. Attinger enters this contract, telling Lockdown to keep his ship in an unpopulated area until the bill passes and they can make their move on Prime. When Attinger tells Joshua about the possibility of getting this Seed, Joshua promises to up Attinger’s share in his company to 7-figures if the Seed is delivered, since he now has big plans for what to do with all the elemental metal he could gain through such an occurrence.
KSI was not only given access to unfunctional Transformers, as there is one he was provided with that still functions. Found injured and trapped within a crashed Decepticon warship, Brains was saved at the cost of his freedom. Now under the domain of Joshua Joyce, Brains is placed within a glass box containing a makeshift miniature stool, bed, and computer; with the computer being hooked up to the memory storage units of Sentinel Prime and Megatron's heads. Brains is forced to decipher the glyph code within their minds, revealing the history and science of Cybertron to KSI, on threat of electrocution. Using this data, Joshua manages to crack the genome of the elemental metal, figuring out how to make it molecularly stable. In this form, the metal works more like nanobots, completely dissolving itself to transform into whatever object it's programmed to become, but with the added bonus that the technology is much simpler than nanobots.
2018 A.D.
Through observing the public discourse surrounding the bill, the Supreme Court justices come to a unanimous decision to pass it into federal law, causing Lennox and - the very pro-Autobot - White House chief of staff to resign from their positions, among many others. The Autobots aren't just stripped of their access to US Military resources, but also their very right to sanctuary within the United States itself. An agreement is arranged with Mexico, however, to grant the handful of Autobots sanctuary there instead. This is all part of Attinger's plan though, with him having the full intention of not letting the Autobots live anywhere on Earth, believing that the world will never truly be safe until they're gone. Attinger puts together a team of like minded ex-military soldiers, including ones who served in Operation Firestorm, led by highly trained assassin James Savoy. The group is named Cemetery Wind and has their establishment played off as the creation of a black ops unit that will serve as the CIA's answer to N.E.S.T..
This is necessary because the responsibility of responding to any and all reports of suspicious alien activity through the 855-363-8392 number, has been transferred to the CIA directly by the wish of the CIA director, and of course, Harold Attinger. His next move is to lure Optimus Prime into a trap so that Lockdown can make his move, but to do this he must separate Optimus from the rest of the Autobots. The answer to this comes in the unfinished negotiations over the matter of where exactly in Mexico should the Autobots be given refuge, with Optimus volunteering to go to Mexico himself to handle it. This entire issue was completely manufactured by Attinger though, with him bribing Mexican President Andrés Manuel López Obrador to accept the agreement with the Supreme Court on unfinished terms, among other things. Optimus is driven in a convoy across the country by Cemetery Wind, who provides his clearance to cross the Mexico-United States border, and then guides him further... into Mexico City.
The full plan is that The Mexican Armed Forces are waiting in "La Plaza de la Constitución" with heavy artillery to ambush Optimus, and while he's busy with them, Lockdown will inflict a mortal wound on Optimus using his special missiles that cut right through elemental metal. Once Lockdown leaves with a still functioning Optimus Prime, the Mexican President will report back to the United States saying that an agreement has been reached and to send the rest of the Autobots into the country. From there, Cemetery Wind will take advantage of the Autobots' likely next move of splitting up to find their leader to pick them off one by one. The American people will never hear from the Autobots ever again, mission accomplished. Once the plan is put in motion though, a complication quickly arises. Optimus Prime makes conversation with the Cemetery Wind operatives through the radio during the long road trip, with this one decision leading to the plan's total failure.
At first, everything appears to be going to plan. Optimus gets absolutely berated by the heavy artillery, especially the mortar shells, and in the confusion Lockdown manages to get three direct hits with his missiles. One of the missiles gets lodged in Optimus's spark chamber, causing his power systems to malfunction. He attempts in vain to transform and drive away, with the Cemetery Wind operatives' job being to block the road, but a mutiny has occurred. The operatives who've rebelled let Optimus through the barrier, then close it behind him and start a firefight with the Mexican Armed Forces to prevent them from getting through. Once the operatives have been put down, Optimus is discovered to be completely out of sight. Needing to disguise himself, Optimus scans a rusted flat nosed semi-truck and then leaves Mexico City, getting picked up by one roadside security camera. Optimus wasn't able to contact his Autobots for reinforcements because all radio transmissions within the city were being scrambled, but once he makes it outside the city he sends out a transmission to his Autobots, saying: "Calling all Autobots! We are under targeted attack! Cease all contact with humans!"
All the Autobots immediately bolt, heading out in all different directions so they can hide before regrouping to find out what happened to Optimus once things have cooled down. Optimus himself resorts to illegally sneaking across the border into Texas to escape Mexico, making his way into a town called Round Rock. He finds an abandoned theater to hide in before his power systems shut down due to the sheer amount of damage they've sustained. Realizing that they're now in serious trouble, Harold Attinger orders the rest of Cemetery Wind (including Savoy who wasn't assigned to roadblocking duty) to work with Lockdown in hunting down the rest of the Autobots, who've at least been picked up by dozens of security cameras. This is done in the hopes of getting Optimus's location from one of them, but after the majority of the handful of Autobots are eliminated over the course of two weeks, no one has talked.
During all of this going down, KSI has made some massive breakthroughs. The molecularly stabilized elemental metal is named "Transformium" by a focus group, and the name is quickly trademarked. All the elemental metal KSI has on hand is turned into Transformium, with it being used to create their own Transformer sentries which Joshua Joyce plans on selling to NASA to aid in space travel and to the US Military to revolutionize armed combat. Only one issue keeps coming up, with it having to do with the centerpiece of the product line: Galvatron. It's modeled after Optimus Prime yet after programming the necessary Transformium to build the model, it keeps turning out different. It almost looks like... Megatron. The POTUS becomes very curious as to how the CIA is exactly going about hunting the Decepticons, so he decides to get a clear answer by sending the new chief of staff to go speak to Attinger and the CIA director in order to get exact quotes.
In the Arctic, Darcy gets a call from the foreman of one of her dig sites, saying that his team has found something that may be of historical significance. When she began the mission to search for elemental metal, she said that if something like this were found, excavation was to be shut down, but the corporate side of KSI was never going to allow this. She immediately gets into a light aircraft and heads to the site, even as the foreman vehemently objects to her doing so. In the rural outskirts of Round Rock, a broke inventor named Cade Yeager gets a call at his house from the owner of a movie theater in town that Cade used to visit all the time in high school, with the owner saying that he's trying to clean the place up if Cade wants to have a look around. Cade calls up his friend Lucas Flannery, who has been surfing on South Padre Island for the last few days, asking Lucas to join him at the theater to help find some potentially valuable stuff. Cade gets in his pickup truck and drives off.