Boris the Animal is an alien belonging to the Boglodite race. Agent K put him in prison. In 2012, Boris escapes and sets on taking revenge on Agent K. Before he goes back in time, Boris threatens the life of Agent K. Agent K’s partner, Agent J, witnesses this and he finds out that K did not only capture Boris but also led the launch of “ArcNet,” a shield put up to prevent the Boglodites from invading Earth.
After his escape, Boris goes back in time and kills Agent K. This changes history and Agent J is the only one who remembers everything. He tries to convince everyone on the Agency that something is wrong but no one believes him. It is not until the newly appointed chief, Agent O, discovers a break in the time-space continuum that the Agency starts believing in Agent J. Due to Agent K’s death, ArcNet was not launched and Earth became vulnerable to the attacks of the Boglodites. J also goes back in 1969 and arrives just as K is about to arrest Boris. J convinces K to investigate and together, they go to The Factory where they encounter an alien named Griffin. At that time, Griffin has the ArcNet. He also has clairvoyant abilities and he senses Boris’ arrival. Griffin is caught by Boris. Agents J and K arrive to save Griffin but Boris escapes them. The Borises from the past and the present meet and form a formidable team of villains.
The two agents bring Griffin to Cape Canaveral, Florida where they will try to deploy ArcNet by attaching it to Apollo 11 rocket. The military prevents them from doing their mission but Griffin manages to convince the colonel how important their mission is for the future. The Borises from both 1969 and 2012 then make a surprise attack on them. The agents defeat the aliens and successfully launch ArcNet. Boris from 1969 is incinerated by the rocket while the one from 2012 tries to make a final attack on K. K is saved by the colonel who takes the shot for him. K kills Boris. After a while, the colonel’s son comes out and searches for his father. Agent K wipes the son’s memory and assures him that his father is a hero. Agent J recognizes that the boy is him and he realizes that Agent K has always looked after him throughout the years.