Sam Witwicky (Shia LaBeouf) discovers something about the origins of the Transformers and their history on Earth after receiving visions from a remaining piece of the Allspark. The evil Decepticons need to capture him for information. The climactic battle takes place at the Giza pyramid complex, where a temple is located within. Lorenzo di Bonaventura explained the film will start before the pyramids were built, tying the Transformers to the beginning of civilization, and implying that "all our heroes end up here because of the Decepticons' master plan." Furthermore, Egyptian hieroglyphs resembling helicopters and other present day vehicles in real life will be explained in the film as being depictions of those Ancient Cybertronians who visited Earth.

Bay explained the battle at Mission City did not expose the Transformers to the public. "Everybody has gone ahead. It's realistic. Two weeks after the tsunami nobody talked about it anymore. It's very weird. We decided to do the same with the Transformers. The government talks about a military thing, says all is false, that it's a joke, and people don't know what they really saw. Orci cited the Phoenix Lights incident as an inspiration for how the Transformers manage to stay covert after the previous film, and added it was an interesting idea for how would the government "hide Optimus Prime". The human soldiers have joined the Autobots' ranks in a team called NEST (Networked Elements: Supporters and Transformers). A government front called McClaren Robotics covers up the robot sightings, and they have an Allspark shard kept in storage in NEST headquarters, in Diego Garcia.