The film's storyline focuses on the discovery of the Ark, a hidden spaceship containing a powerful weapon, and the subsequent battle against the Decepticons. The human characters are mostly focused on Sam Witwicky (Shia LaBeouf) and his new girlfriend, Carly Spencer (Rosie Huntington-Whiteley).
While the official reason for Megan Fox's absence was not publicly stated, it is widely believed that her departure was due to creative differences with director Michael Bay. There were reportedly tensions between Fox and Bay during the production of Transformers: Revenge of the Fallen (2009).
Despite her absence, Mikaela's fate is not explicitly addressed in the film. It is implied that she and Sam have parted ways.