- Sam and Optimus Prime say the title in their lines.
- Megatron is frozen at Hoover Dam, referring to the first battle between Megatron and Optimus Prime (set on the fictional Sherman Dam).
- Optimus carries an energon blade and Megatron carries a flail (both used these against each other in the above battle, while not in this film).
- When the little girl discovers Ironhide in her swimming pool, she is holding a "My Little Pony" stuffed toy. Hasbro owns the "My Little Pony" toyline.
- During the Battle of Mission City, Bumblebee and Ironhide use a "Furby" truck as a shield against Starscream's attack. The "Furby" toyline is also owned by Hasbro.
- A sign reading "Takara Sushi" can be seen during the Battle, shortly after Jazz and Ratchet engage Devastator in combat. The Japanese toy company Takara was responsible for Transformers in Japan until it was sold to Hasbro.
- The voice of Lieutenant Uhura, from Star Trek (1966), saying "Message from Starfleet." The role of Megatron/Galvatron was previously played by Leonard Nimoy and Frank Welker, who have also both played Spock in Star Trek.
- A line, "Across the inanimate vastness of space," was taken from Orson Welles's infamous 1939 radio broadcast "The War of the Worlds". Welles' final film was The Transformers: The Movie (1986), where he voiced the planet-devouring Unicron.
- A phrase from a sermon, "angels from Heaven". In Japan, the Transformers are known as the "Super God Robot Force."
- A line by John Wayne from El Dorado (1967). Wayne's voice has long been associated as an influence on Peter Cullen's voice for Optimus Prime.
- The tail that forms his left shoulder displays a winged sword enclosed in a shield (the emblem of the Air Combat Command) and the letters "FF 1st FW" (indicating the 1st Fighter Wing, based out of Langley Air Force Base).
- A part of the nose that forms his chest reveals a "flying fist" insignia, which belongs to the 71st Fighter Squadron of that 1st Wing (this squadron still flies Starscream's The Transformers (1984) mode, the F-15 Eagle).
- And his tail markings read "ED," which places him at Edwards Air Force Base (he is also seen among a squadron bearing "ED" tail markings).
- Blackout transforms at the SOCCENT base.
- Bumblebee transforms to catch a falling Sam and Mikaela.
- The Nokia phone becomes a Transformer after exposure to the AllSpark.
- Ironhide and Blackout transform in the Battle of Mission City.
- When Starscream flies into space at the end.
- Both films feature similar locations (a dying planet, the Arctic, an underground base, and the Hoover Dam).
- A glowing green artifact from another world plays a prominent part.
- A scene is directly copied where Starscream flies towards the Dam.
- Optimus Prime catches a falling Sam the same way Superman saves Lois Lane (both even say the same line).
- Starscream, like Superman, flies into space at the end.