Spoilers follow.
The narrative context of the vault supports a player's choice of a good alignment early on. The main character's father, James, is a doctor, a profession associated with helping others. Although he has his moral lapses — stealing a child's toy, for example — the impression conveyed is that he is a good person, and it's easy to tell yourself a story about how his values were impressed on his child. In addition, the game reinforces the good path here because most of the "evil" choices you can make in the vault amount to little more than just being a prick. They feel petty, cruel, and pointless. While there are a few threads that can be gathered into a narrative of evil, most of the materials are better tuned for a heroic narrative.
The world itself has the same feel. The ruins of the D.C. area serve as a grim warning about the consequences of war, and the hopelessness that suffuses many of the abandoned areas the character enters argues against the feeling of power V.A.T.S. provides. In addition, most of the people you meet seem to need your help badly. In part this is just a result of including quests, but the world design and NPCs do a good job conveying the impression of desperate people barely hanging on in a hostile land. The few pockets of "civilization" are all in such dire straits, and the character can become a powerful force so early on, that constructing a heroic narrative becomes almost a seamless activity. In addition, some quests are one-sided enough that they simply won't fit in an evil narrative at all.
The story of the good character starts to wobble late in the main quest, however. The central idea of this quest, a giant purifier that will cleanse all the water in the D.C. area of radioactivity, provides a compelling interest, but the antagonist in this section feels like a limp formality. The Enclave enters with completely inexplicable timing, and the behavior of its officers doesn't agree with any goal other than that of a writer who just wants you not to like them. If the Enclave and its brutality had been demonstrated throughout the game world, the case would be more compelling, but this just doesn't happen. The chief problem with the Enclave as antagonists is that they never appear in the open world except as a few harmless wandering robots, until the moment when you are supposed to already be at war with them. This constraint leads the writers to make them act with irrational brutality. James' behavior is also difficult to justify, because his action is so extreme, and the choice he makes to defend the project against the Enclave also renders it useless to his allies.
And why are we to believe that the Enclave is so bad that dying to stop them is worthwhile? The final acts of the game focus on dislodging the Enclave from the Jefferson Memorial so that they cannot start the purifier, but for a truly selfless character it should not matter who starts the machine, so long as it does start. Elements of the game world begin emphasizing the importance of water purification almost as soon as the main character exits the vault. The credit for such a task matters, but does it matter enough to kill dozens of people over it? Why not let the Enclave start the purifier?
The answer to this, of course, is that the Enclave's computerized leader, President Eden, wants to kill most of the people in the wasteland, leaving alive only the people of the Enclave and a few vault survivors. It goes almost without saying that in light of the very low population of the area this idea is hard to credit. A larger problem is that the Enclave officer in charge of the Memorial is one who disagrees with this plan, so much so that the computer asks the main character to carry the plan out for him. Moreover, the game pushes the character towards destroying Eden; dialogue options leading to the destruction of the computer constitute all of the top choices near the end of the conversation with Eden. And once the computer is destroyed, the Enclave seems like less of a threat than ever. The final assault feels less like heroism and more like murder.
The very end of the game presents additional problems. It turns out that the radioactive blast your father used in an attempt to stop the Enclave from taking over the Memorial has still contaminated the control room. Someone must go into the deadly radiation in order to start the purifier. The good character is clearly supposed to sacrifice himself in order to get the project started. However, the good character is also almost certain to have the follower Fawkes, a giant mutant immune to radiation, with him. The reason for this is that you cannot keep Fawkes from following you unless you act like a complete ass. The writers do an infuriatingly bad job of providing reasons why Fawkes cannot save the day. In short, the only way not to feel like a sucker at the end of the game is to feel like a jerk by dismissing Fawkes or sending Sentinel Lyons in instead. The good character's narrative ends with him killing a bunch of people so that he can do something they would have done anyway, and dying needlessly because some giant mutant thinks it's his destiny.
Fallout 3 provides plenty of materials for the player trying to create a heroic story. The family background of the main character supports an ethos geared towards helping others, and the world provides a flock of characters who desperately need help the character can provide. Where this story falls apart is in trying to create a dramatic final confrontation. The effort to rapidly build up the Enclave as an enemy leads the writers to have them behave in odd ways. Ultimately they're never convincing enough as antagonists to really justify the urgency or brutality of the final assault. Then, the final sacrifice is rendered insultingly needless by the presence of Fawkes. The overall experience of Fallout 3 supports a heroic story, but the main character is denied an epic battle for justice. Instead, he gets a series of senseless deaths, culminating with his own.
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