Things were fucked before and are still fucked, Joel doing what he did is just maintaining the current status quo as far as the bigger picture is concerned. But survival is very much feasible in pockets, as Tommy's town shows. The only real ramification would be for Joel and Ellie.
Yet in the first game they made a huge deal out of how vital it was for them to find a cure, and fast because of how badly things were deteriorating.
How do you make an action adventure game out of that? What she finds out, gets super mad and goes off to find the fireflies again and sacrifices herself this time? It'd just be the first game again with a different ending.
10 years after the events of TLOU, Joel and Ellie are living in Tommy's settlement, people have settled in and begun to find more of a sense of normalcy in their day to day lives. They've been forced to defend the settlement a few times from stray raiders, but more and more the threat of clickers has begun encroaching on their home, when it culminates into a full on battle against a horde of clickers that follows a band of raiders who intended to use them as a distraction to break into their home, unaware that they were attracting so many which eventually spelled their own doom.
A huge fight for survival ensues, eventually the the settlement beats them back. An argument ensues amongst the survivors, about how this happened because they've continued to ignore the clickers for so long that the problem has only continued to worsen. The debate continues to escalate with many asking exactly what they were supposed to do about this. Eventually one of the newer groups of survives to settle in this camp mentions that years back they had heard about the government setting up bases up north to study and solve the clicker problem, but eventually a group of the personnel at the base splintered off from them because of disagreements of how to handle the problem, eventually joining the Fireflies.
Some of the younger survivors begin making plans to find this base hoping that the government may have made some strides in their research. They make a plan to find old firefly camps to search for clues of the location of the base. Joel and Tommy object, saying that this base might not even still exist, or they may be struggling to deal with this problem just like they are. Ellie interjects, annoyed at how the conversation has brought up her suspicions about Joel, saying that it's a better plan than sitting around waiting to die at the hands of the Clickers. Determined to go with the group, Ellie prepares to set out, refusing to listen to Joel's objections. Joel, convinced that Ellie will do what she wants regardless of what he says, decides to go with them.
The group set out and find a few camps, bit of information here and their leading them from one to the next. Along the way they are set upon by a mad group of survivors, convinced that the codyceps are a plague released by the planet to punish humanity for destroying the planet via climate change and pollution. This cult is determined to wipe out the last remaining human settlements on the planet, viewing humanity as a scourge that doesn't deserve to survive. These cultists have survived off of cannibalization of their victims, growing even more insane.
During a big skirmish between the two groups, Joel and two other survivors are separated from Ellie and another group. They agree to meet up again at the next camp they had planned to visit. One of the young men Joel is stranded with begins to look up to Joel and idolize his survival skills and sheer determination against the odds. Ellie begins to warm up to one of the young female survivors whose guile and cleverness impresses her. While traveling to the next camp, Joel realizes where exactly they're heading. The camp where Ellie was going to go into surgery to help find a cure. Panicked, Joel increases his pace trying to beat Ellie there, afraid she will find incriminating evidence that will tear his story apart.
Obviously he fails, and Ellie discovers the aftermath of Joel's rampage against the fireflies, she reads old documents detailing the plans the fireflies had for her, and finds Marlene's remains. Joel catches up, and huge argument ensues between her and Joel, infuriated Ellie attacks Joel, and blames him for things getting worse in the world for everyone, because he couldn't let her go. Joel subdues Ellie, and Ellie's new female "friend" intervenes, pushing Joel away from Ellie. Ellie refuses to go any further with Joel, and the groups splinter even further, will Ellie's group going ahead on their own. Joel tails her group, followed by some of the other survivors including the young man who bonded with him, believing Joel to be the best leader to get them where they're going alive regardless of how they feel about what he did.
Along the way there are more ups and downs, with Ellie getting closer to her new friend, and Joel's followers learning more about survival from him, as they fight the cult that continues to interfere with their progress. Ellie and her group wind up destroying a cultist camp a few days away from the army base they're looking for is meant to be, killing many of them who were planning to attack the base losing some of her own people in the process. According to documents they had found in the camp, were planning a huge raid on the base confirming that it is indeed still there and manned by live personnel.
Ellie's group makes it to the goverment base, to find out that Joel and his survivors had beaten her there. Having already explained to the soldiers at the base where they were from, and why. Joel is able to ease passage into the base for Ellie, who begrudgingly is forced to accept his aid. Ellie explains to the scientists and doctors there about how she is immune to the cordyceps mutations and how she could be used to help fight back against the its spread, even at the cost of her own life as she feels responsible for the worsening state of the world. Ellie's now girlfriend, unaware of all this immediately objects, as Joel stays silent believing that it best he doesn't say anything after Ellie's last outburst. The doctors explain that there's no need for her to be so drastic, as they have the proper equipment and skilled personnel that they needn't immediately jeopardize the only other immune person they've found, as she is too valuable to sacrifice without 100 percent chance of a cure resulting from her death.
Ellie is shocked, and discovers that the base has been protecting and developing experimental anti-clicker pathogens and vaccines from research they've gained from studying a young immune boy who has been living at the base. Now that they had an adult subject, they believed they could perform more rigorous and indepth studies that they were afraid to do on the young boy for fear of endangering his life. They assure Ellie that they will do all they can to keep her alive, and that she is more valuable to them alive than dead. After taking a day to process the information they just discovered, Joel catches Ellie alone. They have a heartfelt discussion about the choice Joel made for her, Ellie comes to an understanding about why he did it, after having a talk with her girlfriend about whether or not what Joel did was really wrong given that there was no certainty about whether or not the Fireflies could have found a cure. After everything they were only able to meet and have the experiences they did because of the choice Joel made, even though it wound up having dire consequences. Joel apologizes, and Ellie says that while she doesn't quite forgive him for what he did, she says she understands why he did it and is happy she managed to live to see today.
Seeing that their leaders have made up and have successfully made it to the base alive, the survivors decided to have a small celebration that is suggested by the Major in charge of the base. Unfortunately this doesn't come to pass as the base is suddenly under attack by the cultists. A group of the cultists from the camp that Ellie's team took out had arrived after their battle, finding the remains of their comrades, decide to attack the base immediately, making a loud enough ruckus to alert all of the nearby runners and clickers, leading them to the base. Some of the cultists intentionally allow themselves to be infected, and rush the base. Their leader uses the commotion to break into the building followed by a group of runners and clickers, it is discovered that the leader of the cultists is immune. For whatever reason, the runners and clickers have no desire to attack him, possibly due to his appearance of a highly infected runner. He manages to lead the clickers deeper into the base, cleverly using the clickers and runners as shields against the soldiers, killing many of them and the survivors.
Joel and Ellie manage to rally the soldiers and survivors and beat back the horde, but it is decided that they can't handle a prolonged siege and risk losing the immune. Joel decides that he will lead his team in an effort to reach armaments deep inside the base, hoping to use the explosives and heavy artillery to beat back the infected. Ellie demands to go with Joel, Joel tells her he understands and then proceeds to knock her unconscious, handing her to her girlfriend and telling her to take care of his daughter. Joel fights to the other side of the base, reaching the armory, he instructs his men to take the heavy explosives back with them while he holds the infected back.
Ellie wakes up, and is pissed off that Joel has made yet another choice for her and grabs her rifle, ignoring her girlfriends protests, and go off to back up Joel with her girlfriend following her to back her up. They head up to the top of one of the buildings to get a better view of the base and maybe spot Joel. They hear gunfire and see explosions in the distances, apparently Joel has made to a mounted gun on top of one of vehicles in the base, fighting off the infected and drawing them all to his location. Ellie gives Joel covering fire, doing her best to keep the infected from encroaching behind behind him. As the infected begin to subside, Ellie goes to reload.
Joel is suddenly and viciously stabbed from behind by the leader of the cultists. Joel falls from the gun, behind the truck where Ellie can no longer see him as the cultist continues his assault. Terrified and afraid for Joel, Ellie makes her way down to his position. Joel manages to somehow fight off the cultist leader, but his strength fails him. As the cultist leader goes in to deal the deathblow, Ellie strikes him in the face with the butt of her rifle, having forgotten to reload in her haste, she opts to beat him with it eventually smashing the cultists head into pieces in a rage.
Ellie cradles Joels body as her girlfriend catches up to them. Joel again apologies to her, and says that he's sorry her took her choice away from her again, and that he only ever wanted what was best for his baby girl. Joel dies. Ellie breaks down in a mess, as her girlfriend consoles her.
The remnants of the army regroup, and agree to integrate Tommy's camp of survivors into theirs at Ellie's behest in order to strengthen the bases defenses and share supplies, and the young man who bonded with Joel agrees to deliver the news to their camp. Research continues at the base, and eventually a new antifungal gas is developed that the military believes can be used to wipe out the clickers.
Months later Ellie introduces her girlfriend to Tommy, and tells him how his brother died.
The end.
I don't think I'm a better writer or w/e than the folks at Naughty Dog, but this is kinda sorta what I would have expected from a sequel to TLOU, one that stays true to the themes of the first game but does its own thing.
