"In 1999, an alien spaceship crashed onto Earth. Hidden on board were the secrets of a unique science known as Robotechnology. Databanks found in this ship were transferred to the Earth Robotech Computer Complex. In 2009, an alien search party arrived from hyper-space to reclaim their lost databank. The United Earth Government was forced into an Intergalactic war. Earth forces were able to win the first battle... But at a great cost. The planet was virtually destroyed. New population centres grew out the ashes… It is now 2027. A second armada sent by the aliens is nearing Earth. They have come to recapture the secrets of their lost technology... And then destroy the Earth".
- The narrator's opening monologue to "Robotech the movie".

Some 16 years after the events of episode 36 of "Robotech" (the final episode of the "Macross Saga" arc), the Earth has begun to rebuild and is peaceful again. However the Robotech Masters have arrived to retrieve the memory matrix from the computer that was on board the SDF-1, which crash landed in the Pacific in 1999. A platoon of Bioroids is sent down to battle the humans. Todd Harris, a solider from the Northern Province of the Far East Sector and his squad members, fight off the attack. But something strange is happening. Civilians are being captured alive by the enemy. Colonel B.D. Andrews joins in the battle and fights along side Todd's unit. However Andrews is captured, and the enemy retreats much to the Earth Defence Forces puzzlement.

On their flagship, the Robotech Masters make the surprising discovery that one of the captured humans, Andrews, is a high ranking officer at the Robotech Research Centre where the memory matrix is being held. The Masters decide to make a bio-genetic twin simulant of Andrews, who will be able to follow their orders to the letter. The Masters dispose of the real Andrews and the other captured humans, then send the cloned Andrews down to Earth before any suspicion is aroused to the Colonel's whereabouts. Upon arrival, the clone manages to gain control of the Robotech Research Centre, and goes on TV to deny rumours that the Earth is again at war with another alien race.

Mark Landry, a teenager who works at a motorcycle repair shop, receives a phone call from his friend Todd Harris. Todd is a little agitated, and asks Mark to meet him in an underground car park. There Todd shows Mark a large motorcycle called the MODAT 5. The machine is in fact a new piece of Robotechnology and acts as a database terminal to a giant military computer as well as transforming into a robot. Todd tells Mark that he stole it from the military in order to expose cover-up about the new invasion by Supreme Command and Colonel Andrews. He tells Mark they they must contact "Eve", but their conversation is cut short when Andrews' men come to retrieve the bike. In the confusion Mark escapes with the MODAT 5 and unbeknownst to him, Todd is killed by Andrew's men. An attempt is made to search for Mark and the bike, but he has already disappeared and gone back to the motorcycle repair shop. There he gets the bike repainted red and tells the story to disbelieving workmates.

The next day Mark picks up his girlfriend, Becky Michaels, on his bike to take her to an audition, but the couple fight as he is late. However she forgives him and lets him take her to the audition as he can easily get through the heavy traffic on his bike. He also manages to convince her to give him the number her filmmaker friend, Kelly Stevens, so that he can be cast in her film. Meanwhile a strike force is sent out to battle one of the Robotech Masters flagships. For the Earth forces the battle is a complete disaster. Most of the squad is completely wiped out. The Robotech Masters were forewarned of the attack by Andrews. After the battle, Andrews' proposal to get the alien computer found on board the SDF-1, named the E.V.E, to provide counterattack solutions is given the go-ahead by Supreme Command. He is now in complete control of the memory matrix and gives orders to transmit the entire computer's data to an old abandoned satellite. He explains to his team that this is just to warm up the computer, but they have their doubts. The signals are in fact being intercepted by the Robotech Masters, who store the information in their own databanks.

Kelly Stevens convinces Mark to use the MODAT 5 in the filming of her movie. But Mark is having second thoughts about it. As Mark and Becky film a scene together, pop star Eve appears on a giant screen bellowing out her new hit single and as a result ruins the take. Mark wonders if she is the "Eve" Todd was referring to. Becky is worried about Mark's attitude and wonders if he is in some sort of trouble. After the shoot, Mark decides to ring into Eve's TV talk show to see if she knows anything about Todd and the MODAT 5. But the call is cut short on TV, even though Mark continues talking to Eve for several minutes assuming his call is still being broadcast. Eve suggests that he brings the MODAT 5 to the studio, but on his way there several of Andrews' men in civilian clothes try to capture him. They fail, and soon transformable bike mecha, known as Harguns, and military vehicles are sent in to apprehend him. Mark once again eludes capture after a fight on a highway which destroys most of his pursuer's equipment and sends Mark and the MODAT 5 crashing into a neighbourhood playground.

Mark is unsure if Eve set him up, so he disguises himself as a delivery boy and searches the TV studio for her. What he finds shocks him. Eve is not a real person, but a hologram programmed by a computer. Mark ponders what to do next, but Eve contacts him via the MODAT 5. Eve tells Mark that she is actually a supercomputer called the E.V.E. and that the Robotech Masters have come for her. Supreme Command is trying to cover up the new invasion, but Todd Harris got wind of it, stole the MODAT 5 and attempted to make it public. Someone is sending her data to the Robotech Masters, but she doesn't know who. What she does know however is that once the Robotech Masters have the data, they will destroy the Earth. Eve pleads with Mark to help her and guides him to the underground base where her physical form is.

But once Mark arrives there Eve's transmissions are jammed. Andrews' men discover him and attack in their Hargun mecha. He defeats them, but Andrews himself challenges Mark and both of them end up in a space simulator. But Mark manages to damage Andrews' mecha whicj leaves him vulnerable inside the simulator, which it's gravity core could crush him. Mark makes a deal; if he saves Andrews from being crushed in the gravity core of the simulator, Andrews has to tell him everything. He naturally agrees. Andrews tells Mark that Todd had snapped in battle and wasn't telling the truth, and that he was currently in a military hospital undergoing psychiatric care. Mark refuses to believe him and tells Andrews that he had been talking with the E.V.E. Andrews claims that he created the message to get him to return the MODAT 5. Mark doesn't know what to believe anymore and takes off with the MODAT 5 despite Andrews trying to reason with him to surrender it.

Mark contacts Becky and tells her that she and her friends could be in danger. Becky tries to get more information out of him, but he just tells her that he doesn't want to get her into trouble. Later Mark goes to the taping of TV show where Becky is preforming as a dancer. But Mark is a little miffed when the director of the show, Roger Burke, seems to be putting the movies on Becky. Mark decides to spy on Becky using the equipment on board the MODAT 5. She is staying with the other dancers in hotel, but Roger enters the room and tries to make love to her. Mark is a little enraged at this and uses the MODAT 5 in robot form to break into the room to save Becky. Becky is rather shocked but pleased Mark saved her, but Mark is upset that she thinks that it's all a joke, and slaps her. Becky tells Mark off and walks home.

Meanwhile the Earth Defence Forces try a second attack on the Robotech Masters. Unfortunately since they used the E.V.E. to formulate their battle plan, their enemy already knows the moves they're going to make. It is soon evident that the battle is a failure, and the retreat order is soon given. But the only way out for the Earth battleships is to make a jump into hyperspace as the E.V.E. is in complete control of the main battleship and they can't override the system. The decision to stop transmission of data from the E.V.E. is taken by the staff, but a very angry Andrews forces them to start transmitting the data again. But the staff are very nervous that the enemy could be infiltrating the E.V.E.'s signal and call the head of the Ministry of Computer Science, Professor Daryl Embrey. Professor Embrey immediately orders them to stop transmissions and attempts to have Andrews removed from the project. Andrews responds by ordering his military officers stage a coup d'état against the government. Once he is in complete control, he starts up the transmissions of the E.V.E. to the abandoned satellite again.

Mark decides to make up with Becky. But while they are out having a good time at the flat where Becky and her two flatmates live, Kelly is shot and killed by Andrews men as she completes her film. They take the film of the MODAT 5 and leave Kelly to die. Later, Stacy Embrey (Becky's other flatmate), Mark and Becky discover her body and are horrified. Mark is incensed and vows to kill Andrews. He takes off the MODAT 5 in search of him. Becky comforts Stacy, but her father, Professor Embrey, calls and tells her that they'll have to leave the country for a while. In a last ditch attempt to stop Andrews, Professor Embrey plans to fly to the Robotech Alaska Base where there is an override for the E.V.E. computer. He sends a car for Stacy, leaving Becky all alone. Little do they know, Andrews' men are tailing the car.

Mark travels to the Robotech Research Centre were the E.V.E. computer is. He battles many of Andrews' troops despite being low on ammunition, but eventually he is beaten and left for dead by Andrews himself. Andrews then turns his attention to Professor Embrey, heading to the airport to ambush him and his daughter. Eve wakes Mark and tells him of Andrews plans. The MODAT 5 can no longer move, but Eve tells him that there is a fighter ship close by which can use. Though he is badly injured, Mark manages to defeat the soldiers guarding the fighter. Eve helps to start and launch the the fighter and regretfully tells him that Todd was killed. Mark is angry but she explains that she thought he would be reluctant to help her if he had known the truth. On the way to the airport Becky sees Mark's fighter fly past. Not knowing exactly what it is, and concerned about Stacy's safety, she heads to the airport.

The Robotech Masters have grown impatient with their cloned Andrews and decide to take matters into their own hands. They descend in their flagship to defeat the humans and destroy the planet. But by now E.V.E. has regained full consciousness and forms a battle plan for the Earth troops, who eventually down the flagship and thwart the Robotech Master's plans. The remaining ships in the Robotech Master's fleet retreat and leave the Earth's orbit.

When Stacy arrives at the airport, Andrews begins his attack, taking out not only the tanks protecting Professor Embrey, but the control tower too. But Mark arrives in his fighter and begins attacking Andrews' platoon of military hardware including tanks, robots and other assorted machines. Mark is eventually shot down by Andrews in his Hargun robot. The fighter spins out of control and before bursting into flames, Mark ejects inside his Hargun robot which was hidden inside the fighter. His robot emerges out the flames, but one of Andrews' troops in a Hargun stands in his way. Mark quickly dispenses with him and moves onto Andrews. After a quick but very intense fight, Mark brings him down, and fires a single shot into the cockpit which destroys Andrews and his robot. The fighting has damaged Professor Embrey's jet which has caught fire and is exploding. Stacy is trying in vain to remove a large piece of rubble that has fallen on her father. Mark rescues them both from the wreckage as Andrews surviving men leave in defeat. Becky walks through the rubble looking for Stacy, but to her surprise sees Mark. She runs towards him calling out his name. They embrace, happy that their ordeal is over.