Three Chinese warships are converging on the island of Sainte Marina. Zheng lets Marcus know that it was only a matter of time before someone called his bluff. The captain heads back to the Colorado to engage the Chinese fleet. Sam accompanies him in handcuffs due to his mutinous partnership with the COB. After Marcus has the XO locked up below, he heads up to the Conn where armed men are waiting for him. They are following the lead of Prosser, who relieves Marcus of his command. He also takes both of the nuclear firing keys before tossing the captain into a locked room with Sam.
Serrat and Zheng take over the command station on the island. Sophie throws a monkey wrench into their plans by taking the computers offline. Now Chinese ships can't find a rendezvous point to take over the Colorado. This also complicates things for some crew members on the sub. Prosser learns that his mutiny crew made a deal with Zheng. Their new leader is Hal Anders. When the COB is stabbed in the gut with a screwdriver, Grace grabs a discarded weapon and starts firing. She and Prosser are able to escape from the Conn. They barricade themselves in the torpedo room.
Sam manages to grab a knife when men come to take the captain away. He uses the weapon to initiate an escape. When Anders leaves to deal with the situation, Petty Officer Brannan uses the opportunity to free the captain. There's a gunfight as Marcus and Sam meet up. Brannan holds off the hostile fire until Anders shoots him in the back. Marcus and Sam hole up in an area where they make contact with Sophie. Sam wants her to give the U.S. their coordinates so they can initiate an airstrike on the Colorado. It's the only way to stop it from falling into enemy hands. Sophie knows this means everyone onboard will die.
Serrat is furious. He knows Sophie helped with the airstrike initiative. Zheng wants Cortez to help him convince Marcus and Sam to deviate from their plan. That's not going to happen. On the sub, Marcus and Sam share a moment of levity when they argue about which one of them in more need of a psychiatric evaluation. They take their argument to the intercom where Sam asks their captors to weigh in on the debate. This has an increasingly-agitated Anders planning to nuke Marcus's hometown in Maryland. Fortunately, the captain and the XO still have rudder control.
Prosser lets Grace know that torpedo fuel becomes cyanide gas when it burns. This leads to a plan to deal with the mutinous men who are trying to break into the torpedo room. When the bad guys finally arrive, they see the wounded COB on the floor with a gasmask on his face. A leaking fuel line drips next to him. Prosser flips a lighter to ignite the gas. One man goes down from the poison while Grace takes out the other. She fears Prosser is dead until he gives her a wink from behind his mask.
A desperate Anders prepares to launch missiles on the United States until... CRASH. The Colorado is grounded at the outer shores. Its nose points up above sea level. Anders is injured on the Conn. He sees that the launch has been aborted. The Colorado's angle and depth are outside the necessary parameters. Anders finds Chaplin grieving over Brannan's dead body. The captain turns with a gun in hand. BANG! BANG! BANG! He empties his clip to shoot Anders dead.
Tani lets James know that prospectors infiltrated her family's land. They beat up her brother, wounded her father and killed a friend. They were Zheng's men. She asks James to help her eliminate the problem. If Zheng goes away, the prospectors go away, too. James reluctantly agrees to do as she asks. He sets up in sniper mode to take out Zheng as he prepares to return to China in disgrace. James is truly struggling with what he's about to do. Thankfully, he doesn't have to go through with it. Tani approaches him at the last second. She doesn't want him to be a killer anymore. James doesn't want this either.
Hopper takes the money he got from Kylie Sinclair to Manila where he pays off Wes, who turns over Christine. In Washington, Robert is getting sloshed in a hotel room. Kylie receives a call from her dad telling her to retrieve a gun that's been left for her. The President of the United States then gets on the line. He wants proof of Kylie's loyalty. Robert knows that means she has to kill him. He wants her to do this so she'll be able to prove her allegiance. It's the only way she'll be able to take down those who are responsible for all that's happened. BANG! Robert is shot dead. A horrified Kylie had no choice.
U.S. fighters are still scrambling towards the Colorado. The Chinese are on the way, too. Grace and Prosser are ready to escape the sub at the main hatch. Sam lets Marcus know that it's time to roll, but the captain isn't going anywhere. He's not leaving the Colorado empty. Too many things could still go wrong. Marcus says he's all out of moves, but his XO still has a fight to champion. Sam assures his captain that he will tell the world what they did and why they did it. These two old friends share one final salute with no regrets.
In Washington, Kylie gives Christine the incriminating flash drive. She wants her to tell the press everything. Kylie then heads off to a party where the most powerful people in the country have gathered. Her father tells security that she's one of them, so there's no need to search her. Kylie gives her dad a kiss before moving over to the special guest in the center of the room. She calls out to the President of the United States. Kylie then pulls out a hidden gun. BANG! She shoots the president dead.
Sam, Grace and Prosser make it to shore. They see the fighters lock in on the Colorado. Aboard the sub, Marcus dons the sunglasses he wore when he and his crew last crossed the equator. He lets out a little laugh. The fighters fire missiles at the Colorado. BOOM! It's a direct hit resulting in a massive firestorm. The Colorado and its captain are no more.
Sam addresses to the press corps that's waiting for the Colorado crew when they return to American soil. He speaks of his captain. He speaks of their mission. He speaks of their long journey to get back home. He fights through the crowd when he sees Christine. The two of them hug each other like they never want to let go. For the first time in a very long time, Sam knows that he truly is home. As for the Colorado, the sub was ultimately lost at sea as was its captain, Marcus Chaplin, who is also now truly home.