ACT ONE

Out of Time: Upon waking up from his second round of cryostasis, Shepard gains control of the wing and opens Nora's stasis pod. He reluctantly takes her wedding ring, holding it close as he vows to find the people who killed her and get Shaun back. As he wanders through the abandoned vault, he learns that everyone else is dead. Stricken by further grief, the sole survivor finds his way to the surface via the Overseer's office and an abandoned Pip-Boy. He returns to his ruined home, where Codsworth greets him and helps him search the neighborhood for signs of his family. When the duo are unable to locate Shaun, Codsworth suggests asking the settlers at the nearby town of Concord. On his journey there, Shepard finds Dogmeat (who earns the name by stealing food from Shepard's hand while he rests). The duo travel to Concord, where an intense battle between the Raiders and Minutemen, with the latter's leader calling out to him and pleading for help. Shepard takes up arms and fights his way through the Museum of Freedom.

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When Freedom Calls: After fighting through the Museum of Freedom, Shepard finds himself face-to-face with a handful of survivors calling themselves the Minutemen. The group's leader, Preston Garvey, introduces them all and turns the conversation to his handyman, Sturges. Sturges lays out his plan to deal with the remaining Raiders by stealing a suit of T-45 power armor from the crashed vertibird on the museum's roof. Shepard, having experience with this armor, agrees to help them by powering up the armor and collecting it. He engages the Raiders and drops down from the museum's roof, triggering a series of loud banging noises from the sewers. As the last of the Raiders is wiped out, a vicious deathclaw bursts from the sewers and attacks Shepard, who struggles in defeating the creature. Eventually, he succeeds and re-enters the museum, catching up with Preston and his group as they discuss their plans to move to Sanctuary Hills. During this conversation, Mama Murphy pulls Shepard aside to reveal that she knows he is looking for his son and that she can "feel his energy", though she is unsure where. She points him to Diamond City, though Shepard offers to escort the group to Sanctuary Hills before heading out.

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The First Step: When the group arrives at Sanctuary, Preston Garvey pulls Shepard aside to thank him once again for his help. He also asks if, considering what he's done so far, if he would help him rebuild the Minutemen. Shepard asks more about the faction before agreeing, to which Preston directs him to a nearby settlement that has been having trouble with Raiders. Upon helping the settlement, Shepard returns to Sanctuary and talks to Preston about how the journey went. Preston congratulates him on his success and offers him a flare gun and several flares, telling him that the Minutemen will always be prepared to join him where he needs them. He then tells Shepard of how the Minutemen's forces dwindled, to which Shepard reassures him and lets him know that, as General, he will do everything he can to avoid that kind of catastrophe from happening again. The two end their talk on good terms, and Shepard spends the next few hours establishing reliable food and water sources for the new settlement.

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Jewel of the Commonwealth: After ensuring the Minutemen survivors settle into Sanctuary, Shepard makes his way to Diamond City. Upon reaching the entrance of the settlement, he's promptly roped into a confrontation between Piper Wright and Mayor McDonough, acting as a scapegoat for the city's guard to open the gate and let them both in. When meeting the mayor face-to-face, Shepard asks who he can talk to about the case of his missing son, to which he learns the city will refuse to stick their nose into the matter due to their own abundance of missing persons cases. Disgruntled, he curiously follows Piper to her agency and follows up on their brief conversation, ultimately agreeing to do an interview in exchange for the information. Shepard tells Piper the whole truth of his circumstances, and she points him to the Valentine Detective Agency. Unfortunately, his luck runs out as his secretary, Ellie Perkins, tells Shepard that Detective Valentine himself has gone missing. Reluctantly, Shepard agrees to help locate the detective.

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Unlikely Valentine: Following Ellie's notes, Shepard finds himself at Park Street station. He fights his way through the subway station, stumbling across the entrance to Vault 114. Within the vault, Shepard finds himself eavesdropping in on a conversation between Dino and Valentine, where the cunning detective convinces Dino to run off and square off his gambling habits with the group's leader. Shepard sneaks by to free Valentine, who informs him that they should leave as soon as possible. The duo briefly discuss the case of Shaun, though save the chit-chat for later as they fight through the vault and discover the leading duo: Darla and Skinny Malone. Shepard takes the lead, convincing Darla to leave and Skinny Malone to let himself and Valentine leave peacefully. The duo get out unscathed, and make their way back to his office in Diamond City.

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Getting a Clue: At the Valentine Detective Agency, Shepard makes a formal report with the detective regarding the disappearance of his son. Valentine suspects a notorious mercenary named Conrad Kellogg is behind the incident, and the duo begin their hunt by investigating kellogg's house. Shepard finds himself at the mayor's office to ask for a key, where he ends up being dismissed by McDonough for "sticking his nose in places they don't belong". Dejected, Shepard begins to leave and is stopped by Geneva, the mayor's secretary. She inquires about his visit, in which Shepard manages to bribe her for a copy of the key. Now in Kellogg's home, Valentine and Shepard find a secret room full of Kellogg's personal belongings. Dogmeat sniffs at the cigars then sits by the door, eager to follow Kellogg's trail. Shepard says his goodbyes with Valentine, telling him that the matter is too personal and that he needs to confront Kellogg alone.

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Reunions: Dogmeat and Shepard retrace Kellogg's steps throughout the Commonwealth, finding bloodied rags, the remnants of an Assaultron, and a sleeping deathclaw. Ultimately, this harrowing trail ends at the doorsteps of Fort Hagen. Utilizing the entrance in the underground parking lot, Shepard pauses as Kellogg addresses him via the building's intercom. The mercenary advises him to turn back, which he refuses. Their conversation grows more hostile, with the mercenary taunting Shepard. Eventually, he reveals that Shepard will never get his boy back given the fact they're with the Institute, far underground and far out of reach. Shepard confronts Kellogg, with their conversation resulting in an intense gunfight and the death of Kellogg. After examining the mercenary's corpse, Shepard finds the password to a nearby terminal and a cybernetic brain augmenter, which he takes both, unlocks the security doors, and returns to the Valentine Detective agency.

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ACT TWO

Dangerous Minds: Back at the Detective Agency, Shepard, Valentine, and Piper discuss what happened and their findings. Upon learning of the cybernetic brain augmenter, Valentine suggests they take a trip to locate Doctor Amari in Goodneighbor, a fortified settlement tucked between the ruins of Boston's Financial District. Shepard agrees and takes Valentine along, promising Piper he'll be back to fill her in on his progress. Upon finding Doctor Amari in the Memory Den, Shepard and Valentine are placed into a simulation utilizing the remnants of Kellogg's brain (attached to the augmenter) to relive Kellogg's final memories and piece together information that will point them to the Institute. During this dream-like state, Shepard learns how similar his circumstances were to Kellogg's, and of a scientist by the name of Virgil, who escaped the Institute just before a now-child Shaun was handed into their custody. Disoriented, Shepard takes a moment to rest before speaking with Doctor Amari about Virgil. She informs him that Valentine is upstairs already. When talking to Valentine, Kellogg's voice takes over and once more taunts Shepard, leaving him in a defensive state when Valentine regains control of his processes. Apologetic for the scare, Valentine offers to continue accompanying Shepard. The sole survivor declines, stating that it's nothing personal against Valentine. He once more says his goodbyes, then stays in Goodneighbor a few days to gather supplies for his journey to the Glowing Sea.

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The Glowing Sea: Following the freeway southwest, Shepard finds himself staring down the ticking Geiger counter on his Pip-Boy as the world around him dies. Storms rage over the horizon, and mutated creatures seem to hold free reign over the unoccupied ruins of the Commonwealth. As he travels, Shepard finds himself close to the Crater of Atom, a site holy to the Church of the Children of Atom. A woman by the name of Mother Isolde takes the newcomer aside, informing him that he is trespassing. Shepard tells her he doesn't want to hurt her people and, though thoroughly confused by their worship of radiation, that he just wants to find where any caverns in the area may be. She gives him directions over a nearby ridge, where the sole survivor finds Virgil in the form of a Super Mutant. Virgil offers a proposition: In exchange for his knowledge, Shepard must locate a serum within the Institute. After the deal is agreed upon, Virgil points Shepard toward the C.I.T. ruins north of Diamond City, stating that the sole survivor must kill a Courser to gain their chip for teleportation access.

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Hunter/Hunted: Finding the ruins, Shepard tracks the "courser signal" east toward Greenetech Genetics, an abandoned laboratory full of mercenaries who are attempting to hunt down the courser before it kills them all. Weaving through the battle, Shepard finds the courser up on the seventh floor, threatening some of the mercenaries for a password before being executed. The courser pauses when he catches wind of Shepard's appearance, asking what the sole survivor wants. Not letting him know, Shepard engages the synth in combat and loots the chip off of his body. A woman calls out to him as he's about to leave, and Shepard helps her escape the room she's trapped in. She reveals to him that the courser was hunting her down, with her being a synthetic escapee from the Institute. He lets her go, wishing her well, before making his way back to the Glowing Sea.

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The Molecular Level: Now able to take the next steps, Virgil directs him to the Railroad, a group of mercenaries set on liberating synthetic beings from the Institute and giving them lives within the Commonwealth. Shepard follows the Freedom trail and makes contact with the group, who reluctantly agree to decrypt the data on the chip. Of course, this act comes with a price: They must be the ones to maintain hold on the data once it's decrypted. Shepard lets them keep the chip, only taking the code he needs so that he can utilize the signal interceptor plans to travel to the Institute. However, the machine's schematics are far beyond his technical skill, so he returns to Sanctuary and enlists the help of Sturges and the Minutemen. They aid him in building the signal interceptor, and see him off as he takes the voyage to the Institute.

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Institutionalized: Once successfully appearing within the Institute, a voice greets him through the intercom system, inviting him to take the elevator adjacent from his entry point. Before he does so, Shepard loads Sturges' holotape into the nearby console and acquires the data asked for by the mechanic. Shepard then follows the voice through the empty Institute corridors and up another elevator, only to find what appears to be a 10-year-old Shaun held in a cell. Shepard confronts the boy, who calls out for Father, scared and confused. The sole survivor's reassurances fail, and Father steps out of a nearby room to shut the synthetic boy down using a code phrase. Distressed by this, Shepard demands to know where his real son is, to which Father reveals himself to be the real Shaun, director of the Institute. He too reveals that it has been over 60 years between his kidnapping and their introduction, which is how Shaun appears to be older than his father. From there, he says that his own circumstances are fair, and that he's enjoyed his upbringing. Shepard tries to understand, and agrees to tour the Institute in hopes that his mind will change. Unfortunately, seeing the Institute in operation does little to convince Shepard that it is a good thing, though he agrees to do minor jobs as a way to connect with his son. It is through this work that Shaun learns his of his father's experiences in the wasteland, and his discomfort with the Institute's mode of operations. The breaking point comes after Shepard lets the captured synths at Bunker Hill go, to which the duo meet on top of the C.I.T ruins and have their final conversation. Shaun banishes his father from the Institute, stating that his efforts to aid the wastelanders are wasteful and that they will never be appreciated. Knowing he cannot change his son's mind, Shepard ends their conversation, telling Shaun to consider alternatives and that he is disappointed in the man Shaun grew up to be. Returning to Sanctuary, Shepard hands the data over to Sturges and isolates himself from the group, briefly returning to Vault 111 to grieve the loss of his son beside the chamber he found Nora in. He takes this time to give Nora a proper memorial within the vault and within Sanctuary, where he refuses help from the others during the process of burying her and memorializing her.

Taking Independence: After taking time to recuperate from the loss of his son, Shepard begins recruiting a number of settlements to the Minutemen cause. While accompanying him on his mission, Preston brings up the idea of retaking the Castle via assembling a strike force and propping up a radio transmitter. The strike force opts to take a direct approach to clearing out the mirelurks. Once the initial nests are cleared, a mirelurk queen emerges from the lagoon and begins attacking everything in sight. With her defeat, and numerous casualties, the Castle is reclaimed by the surviving forces. Shepard spends the day tinkering with the radio transmitter, and eventually powers it upto send their message through the Commonwealth. Approximately three days later, Ronnie Shaw arrives and sends a message out for Shepard directly, asking him to meet with her when he has the chance.

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Old Guns: Shepard arrives at the Castle to meet Ronnie Shaw, and she informs him of an armory hidden in the west bastion of the Castle that only she knows how to access. The duo take an alternate entrance (a tunnel in the former general's quarters) and navigate trap-laden corridors to find General McGann's corpse and the armory access. Shepard takes the former general's uniform after Ronnie's suggestion, and the duo work together to build some artillery. After a series of test fires, the duo arm the Castle with these new artillery bastions.

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Defend the Castle: With the completion of the Castle's fortification, gunfire suddenly breaks out as waves of Institute synths and coursers teleport in to take down the threatening force. Knowing now that Shaun meant what he said about betrayal, Shepard sticks alongside Preston and Ronnie Shaw to defend the Castle from destruction and reclamation by the enemy forces. After the battle concludes, Shepard pulls Preston aside and lets him know what transpired at the Institute. The duo discuss a plan to take them down, to which Preston agrees to help him, stating that he's done more than enough to help the Minutemen, and that it was the least he could do for a good friend.

The Nuclear Option: Once the duo considers the Minutemen ready to take on the Institute, they speak to Sturges, who has since completed his analysis of the Institute data Shepard brought back. They discover a possible backdoor into the Institute: an old cooling water tunnel system just south of Ticonderoga. Shepard utilizes the power armor suit he kept from his first encounter with the Minutemen, guiding the Minutemen forces through the tunnels and breaking through to the Institute's Relay control room. Shepard loads the targeting sequence into the central console, teleporting the rest of the forces in behind him. Preston hands Shepard a fusion pulse charge, and the Minutemen fight Institute forces down toward the reactor room. However, one last hurdle remains: Access to the reactor room via the Advanced Systems department. Making his way up the central elevator, Shepard finds Shaun laying in bed, dying. He hesitantly approaches, lowering his gun and pleading for him to make things right by helping him launch the evacuation notice. Shaun reluctantly hands over the terminal password, telling him that there is nothing more to be said between them and to let him die in peace (re: alone). Shepard launches the evacuation notice and unlocks the access point, says goodbye to Shaun, and leaves to join the fight for the reactor. The reactor is armed with the pulse charge, and the remaining forces make it back to the Relay room to escape. As they prepare to teleport out of the Institute, the young synth modeled after Shaun appears, begging Shepard to help him escape and to not abandon him. Much as it pains him knowing this Shaun isn't the real one, Shepard takes the boy into his arms and steps into the Relay with him. Now on the rooftop of the Mass Fusion building, he says nothing as he detonates the charge and blows up the Institute's reactor. After the debris settles, he talks to Preston, who celebrates their work and gives him space to cope with what has been done.

All Aboard: Between aiding the Minutemen and rebuilding the areas surrounding the Commonwealth, Shepard receives a radio broadcast from the Nuka-World transit center. Remembering the theme park from his pre-War days, Shepard curiously investigates the signal to find Commander Kaylor and a team of Gunners scoping the parking lot. Fighting them once they open fire on him, he heads inside to find an injured man claiming that the Raiders took his wife and children. Shepard administers aid to Harvey, who thanks him and urges him to power up the station and take the monorail. Upon entering the park, the pre-recorded tour is interrupted by Porter Gage, who sarcastically wishes the man luck in surviving the deathtrap before him before stating that, should he survive, the two should talk.

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Taken for a Ride: Arriving at the Nuka-Station, a raider by the name of RedEye will announce that the Gauntlet has begun. From here, Shepard faces a whole new kind of personal Hell. Traps lining every inch of exposed concrete, radiation barrels that cause Shepard to double over in agony and hurl, intense mazes, a sealed room that slowly fills with gas and chokes him out, and finally: a confrontation. Within the Cola-Cars Arena stands Overboss Sloane (aka Wildfire). Upon entering the locker room, Gage talks to Shepard again, telling him that he's been through the ring before and, frankly, doesn't expect he'll survive Sloane's fury and that, were circumstances different, he might have helped him. With that, Gage sends Shepard on his way and watches as the battle commences. Shepard manages to take Sloane down, though chooses to spare her for the time being as he has no interest in taking her position as Overboss. Try as he might, though, he is unable to turn back and leave, so Sloane has men capture him and bring him to the Market until she recuperates.

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Open Season: While in the Market, Shepard finds himself talking with other wastelanders who have been unfortunate enough to survive the trials the Raiders put them through. One such survivor is Mackenzie Bridgeman, who urges him to help save them, and the Commonwealth, by taking out the raider leaders. She helps remove the bomb collar from his neck, and tells him where the three leaders are located. He starts with Mason, the closest of the three, then Mags and William, then finally, Nisha. Once the leaders fall, all of the Raiders open a free-for-all hunt on Shepard. Gage and Sloane don't join in, instead opting to fall back by leaving the main park's grounds and taking shelter within the old Hubologist camp (now abandoned after Sloane executed the group). Once the deed is done, and the Raiders are presumed dead, Shepard returns to the Market to inform Mackenzie of the plan's success. The duo help free the traders, who establish their own settlement at Nuka-World.

Far From Home: After stopping the thread of Nuka-World Raiders, Shepard returns to the Commonwealth to find a message from Ellie Perkins pertaining to a new case. He travels to Diamond City and is sent to the residence of Kenji Nakano to follow-up on a missing persons case. Upon reaching the residence, Shepard meets with Kenji and his wife, Rei. They inform him that their teenage daughter, Kasumi, has gone missing, and that they need his help finding her. After a thorough talk with both parents, he follows a trail of clues to the family's boathouse, where a safe reveals plans for Kasumi to make contact with a colony of synths near a northern location called Far Harbor. Their contact has ultimately led to her questioning her own humanity, so much so that she ran away to discover the truth. Upon hearing the news, the Nakano family begs Shepard to retrieve her daughter, offering for him to use their boat to reach the harbor. Promising to help the best he can, Shepard sails off.

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Walk in the Park: Upon reaching Far Harbor, Shepard is greeted by two locals, Captain Avery and Allen Lee. He informs the duo that he's following investigative leads about Kasumi, and learns that the teen had crossed through the harbor. Their conversation is cut short by the threat of enemies outside the "Hull", and Avery promises to answer any questions the sole survivor has if he helps protect their settlement. After a harrowing battle, Avery and Allen converse with Shepard about the Fog surrounding the town, to which Allen attributes blame to the Children of Atom and the synth colony, Acadia. Avery directs Shepard to find Old Longfellow, resident of Far Harbor and expert navigator. Old Longfellow is found within the town's bar, and seems displeased as Shepard inquires about hiring him as a guide. Shepard reassures him that he won't slow the navigator down, and Old Longfellow begrudgingly agrees to help him reach Acadia.

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Where You Belong: Shepard enters Acadia and is greeted by the settlement's leader: an old synth named DiMA. The synth lets Shepard know that Kasumi is there, and directs him to the teen's location as an invitation to explore the rest of the colony. Upon meeting Shepard and learning he came for her, Kasumi affirms her belief that she is a synth and that, though in a hushed tone, she believes that there's a secret behind Acadia's formation. Shepard curiously follows her leads, opting to eavesdropping on the founders' conversation to learn DiMA gave an old nuclear submarine to the Children of Atom as a home base. Within this base are DiMA's old memory files that, should they be discovered, will put the island's two factions (Far Harbor and the Children of Atom) on a war path with one another. Shepard confronts DiMA with this knowledge.

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Best Left Forgotten: DiMA seems ashamed that the truth has gotten out, and that the circumstances have spiraled as far as they have. He doesn't say much else, though after hearing their own talk, Kasumi suggests that Shepard investigate his memories by infiltrating the Nucleus Command Center himself. Stopping by Far Harbor to stock up on radiation prevention, Shepard sets out to the Nucleus and infiltrates the base, inserting himself into a virtual, maze-like environment to access DiMA's memories. Now armed with the coordinates to DiMA's secret medical facility at the Vim! Pop factory, Shepard sets out to investigate.

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The Way Life Should Be: Upon investigating the Vim! Pop factory, Shepard finds an unmarked grave at the center of the secret medical facility. Taking a moment to rest, Shepard contemplates if these memories are really worth exhuming the grave, and the consequences that will come with the truth coming to light. He hesitantly approaches the grave and exhumes it, finding the body of the real Captain Avery. Horrified, Shepard steps back to listen to the holotape (What's Done is Done), and learns that DiMA killed the real Captain Avery to replace her with a synth, who would act as his eyes and ears within Far Harbor. Shepard returns to Acadia to confront DiMA, telling him that he needs to turn himself in and be honest with Far Harbor's residents. The sole survivor leads DiMA to the settlement, and helps the townsfolk put him on trial. Allen Lee attempts to incite the entire town against Acadia, revealing to Shepard that DiMA was not wrong in his assumptions regarding the townsfolk's reactions. Though he tries, Shepard fails to talk the townsfolk down, and they march on Acadia, burning it to the ground where it stands. In the conflict, Kasumi is killed.

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Close to Home: With the blood on his hands, Shepard leaves Far Harbor and returns to the Commonwealth, where he must face the Nakano family and bear the bad news. He informs Kenji of her death, only able to ask if he truly wants to know upon the father's demands to know what happened. Stricken by grief, Kenji asks Shepard if Kasumi's ramblings about being a synth were false, to which the sole survivor responds that he doesn't have a definitive answer for him. Kenji tells Shepard to leave, and the case is closed.