The movie starts off with Alex Hopper (Taylor Kitsch), long haired and unshaven in a dirty t-shirt in a bar drinking. It's his birthday, and his older brother Stone Hopper (Alexander Skarsgård) buys him a shot and a little cupcake with a candle. Stone sees Alex eyeing a pretty blonde girl and urges him not to waste his wish on a girl but to wish for a job. Alex blows out the candle and stumbles over to the girl. The girl is Sam (Brooklyn Decker), and she's hungry. The bartender tells her the kitchen is closed even though the "kitchen" is just a dirty microwave. Sam wants a chicken burrito. Alex tells her to give him five minutes. He runs across the street to a quick-mart that is closing. He tries begging the clerk to let him go in a buy the burrito, but she shuts him down saying "It's too late to eat a chicken burrito, too many complex carbs." Alex is determined to get Sam her burrito. Through a silly series of surveillance camera reels, Alex is shown climbing to the roof of the mart and falling through the ceiling. He gets the burrito and tries to crawl back out through the hole he made. The police show up and Alex is seen rushing back towards the bar. The police order him to stop and when he doesn't, they tase him. He's still determined to get Sam her burrito, so he crawls towards her and proudly puts the burrito in her hands. He has a goofy grin on his face until the cops tase him again.
Alex wakes up in a bath tub filled with ice water to hear Stone yelling at him. Alex has no job and has been living on Stone's couch. The girl Alex was trying to impress was a Navy Admiral's daughter. "Now you're messing with my job!" He tells Alex that its time for a new plan: he's joining the Navy.
Skip to a bit later and we see that Alex has cleaned up very well. The Navy has gathered with military from other countries for RIMPAC, which is war naval games/exercises. They also play soccer. Alex is playing hard and goes to kick in a score when a member of the rival team kicks him in the face. Stone tries to get someone else to take the penalty kick, but Alex is belligerent and takes the kick himself. He misses, and the USA loses the soccer match to Japan. This shows more of the tone of Alex's character. He is smart and capable, but he's too proud and over confident.
Later, Alex and Sam are on the beach, and Sam wants to know how Alex intends to ask her father, Admiral Shane, for her hand in marriage.
The next morning, Alex and Sam are rushing to the Naval yard. Her father is giving a speech to commence RIMPAC. Even though they are late, Alex stops to detail the difference between a battleship and a destroyer to a young tourist.
After the speech, Sam tries to get Alex to ask her father for permission to marry, but he is too nervous. He goes into the restroom to splash water on his face and practice his lines again. As he turns to leave, the Japanese Naval officer that kicked him in the face enters. They talk smack before smacking each other around. Another officer hears the commotion and goes for help. Admiral Shane is very angry as the two men try to say they weren't fighting. They lie and say Alex slipped on some water and the other guy tried to catch him, and they knocked heads and then fell into the walls. Admiral Shane dismisses everyone but Alex. The Admiral begins a quote by Homer which Alex finishes. The Admiral says "The fact that you know that infuriates me!" When asked if Alex has anything to say, he says no and is dismissed.
Stone tells his little brother that he has really messed up this time and most likely he will be kicked out of the Navy once RIMPAC has concluded. Alex begs his brother to make some phone calls, but Stone tells him there are no calls to make.
Stone commands a ship while Alex works in the defense room of another ship. Their speeches to their crew are intercut with Stone saying that this a learning exercise and urging his people to just do their best. But Alex says that they are not there to learn they are there to win and anything less than is unacceptable.
The ships are sailing out to sea when a sailor spots something in the distance. He informs the bridge, but they can't see anything on their radar. A camera gives us the first glimpse of the alien ship. Alex and two other sailors take an inflatable boat out to investigate. Alex gets out of the boat and against the advice of Raikes (Rhianna), touches the ship which shocks him, throwing him backwards. Raikes pulls him back into the boat and they try to leave, but the boat won't start. The alien vessel sends up a signal into the atmosphere that creates an impenetrable dome. A fighter jet is seen smashing against the barrier. The alien vessel scans the ships trapped inside the dome and starts firing weapons at the heavily armed ships. Alex watches as his brothers' ship is destroyed. Alex and his crew finally make it back to their ship and it's discovered that the senior officers have been killed, which makes Alex in charge. He orders a full-out attack on the ship even though there are men in the water who need rescuing. He is finally persuaded not to attack and rescue the men.
Back on land, Sam is working with an Army patient who has lost both of his legs. He is irritable and not interested in trying. Sam tells him to put on his legs and that they are going for a walk. She takes him hiking up a mountain that he tells her his dog, Mustard, could climb. She asks if he walks a lot with Mustard to which he responds "Mustard's dead."
While they are hiking, police in jeeps drive up and tell them to get off the mountain. Instead, they follow the trail so that they can see the aliens. When they catch up with the jeeps, they find all the police dead and the vehicles blown to bits. The aliens are walking around and almost find Sam but are distracted by a horse. Sam and her patient find a scientist who had been monitoring a communication tower that the aliens have hijacked. He tells them that they are going to use the deep space satelite to send a communication to their home world and that more ships would come. He also tells them that he has a way of getting a message to the war ships out on the water.
Back on the ship, Alex is mourning his brother. A sailor tells him that he is needed now, and they go to where the body of an alien has been fished out of the water. Alex and the Japenese captain work together to remove the alien's helmet. They are humanoid creatures with pale spines jutting out of their chins. Alex tries to look into the alien's eyes with a flashlight, and it wakes up. It grabs Alex by the face and somehow Alex is able to see their plan, which is to conquer Earth. Things get hairy when three other aliens show up to rescue their buddy. They are undetectable on radar and to sonar equipment. Alex and Raikes chase the aliens through the ship, but they get away. Alex gets the message from Sam that the communications tower needs to be taken out before 8am when the satelite will be in alignment to send the transmission. Then the aliens destroy Alex's ship, but they manage to survive and scramble into the life boats.
Alex gets the bright idea of using the USS Missouri to complete his mission. The Missouri is a decades old battleship with an outdated steam engine and none of the young sailors know how to operate the ship or her weapons. Thankfully, there are several retired veterans aboard, and in a beautiful moment, Alex tells them "You've already given so much, we have no right to ask more." But the veterans rally under him, and they get the ship underway. The Japanese captain uses a water displacement method to track where the aliens are, and they begin to attack. The idea is that the humans can't detect the aliens and the aliens can't see the humans until they deploy weapons. The water battle is exciting with Alex using unconventional methods to win. However, the communications tower is still active, and it seems that the aliens will succeed in sending their message until Sam drives a jeep through the power cables, delaying the message. This gives Alex enough time to launch their one remaining missile. Before he can, the aliens dispatch two mega-weapons that will sink the battleship, killing everyone on board. Alex makes the decision to sacrifice himself and the crew to save the planet. But once the tower is destroyed, the mega-weapons power down and fall harmlessly into the water.
At an awards ceremony, Admiral Shane presents Alex with an award for his late brother as well as one of his own for his outstanding job. Alex finally gets up the courage to ask Admiral Shane for Sam's hand in marriage and....the Admiral says no. He tells Alex that he's hungry and that he wants a chicken burrito. They walk off together with Alex asking the Admiral "She told you about that?"
After the credits....
Three young Scottish lads are walking down a lane when they see a crashed alien vessel. They excitedly investigate, and a workman pulls up in his truck with a variety of tools. They encourage him to try and get into the spaceship. After a few humorous attempts, the vessel is opened and out pops another alien, scaring the humans.
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