I see the potential in the story that was presented, but the execution was still incredibly bad. It's like Tim Kring... maybe Carter is good to have for ideas, but he doesn't know how to bring those ideas to the screen in a way that makes any amount of sense.
Since I'm sitting here with some free time, allow me to take you through my version of the season finale...
For starters, I would rewrite the premiere. No alien DNA. CSM would not appear. Scully would check Svetta's DNA and find nothing alien. They can still find something anomalous, but the alien aspect doesn't really seem necessary... If the plan is to remove things from people's DNA, disabling their immune systems, then all they would have to do in order to save people like Scully is... not f*** with her DNA!
Okay, so the finale...
Scully's voiceover as we saw it, ending with her turning into an alien. Only, I would have her wake up from that dream. Show us that it's been on her mind, and that it's something that scares her. I might have played up some of the violence and victimization that she suffered over the course of the original series. She is a strong woman, but she's been through hell.
Scully shows up in the basement office, but Mulder is nowhere to be found. She finds the laptop with the Tad video on it, and presses play. He isn't as frantic as he was, but he also isn't in his studio. He is recording his video from a cell phone, talking about finally discovering proof that the government has been genetically experimenting on American citizen ever since the beginning of the smallpox vaccinations. During the video, he would make reference to the children that Mulder and Scully investigated in episode 2... he has been in contact with Mulder. Scully looks at her watch, looks around the office once again because Mulder should be there, and then walks out.
Scully walks into Skinner's office and takes a seat. Skinner asks where Mulder is, and Scully says that she has no idea. Skinner can't help but smile at that. They've started off countless meetings the same way. Before they get down to work, there is a knock at the door. Agent Miller walks in. Skinner asks where Agent Einstein is, and Miller replies by saying that he doesn't know. Scully and Skinner look at each other.
In a hospital (preferably one that doesn't look like something from a 1950's horror movie), Mulder begins to regain consciousness. He is pale and sweaty, and at first, he thinks that Scully is sitting beside his bed. He smiles. But as his vision clears up, he realizes that it's Einstein. His smile fades considerably.
She explains that Mulder was found on the side of the road the night before, beaten and delusional. The police found her card in his pocket, and called her. At first, she assumed that he was on another mushroom trip, but something else is going on. His brain scans are irregular somehow (insert medical mumbo-jumbo here) and he is fighting off a severe infection of some sort. His blood work is insane. She's having it run again, because it looked like he was infected with about three types of disease, all of which should be covered by his vaccinations.
Mulder wants Scully. Einstein says that Scully is her next phone call, but before that happens, she wants to know what the hell is going on. What happened to Mulder on that street?
Mulder says that Einstein needs to get Scully now. He tells her to let Scully know that "He's alive. The son of a bitch is alive..."
"Who?" asks Agent Einstein.
Cut to some time later. Scully and Agent Miller arrive at the hospital. Scully gets an update from Einstein, including the information that “Some cigarette smoking man is still alive...” Einstein has no idea what that means, but Scully stops walking and says, “You have to be kidding me.”
When she sees Mulder, he tells her that he was supposed to meet with Tad O'Malley at his house the night before, but when he got there, his house was a mess and O'Malley was gone. His bodyguard was dead on the front porch.
Mulder was attacked by a man who tried to use chloroform on him, but Mulder fought him off. He couldn't get to his car, so he ran for his life. That's when he was found on the road and brought to the hospital.
Scully asks about CSM, and Mulder tells her that he saw him as he was being loaded into the ambulance. He was there, smoking his cigarette through a hole in his neck and talking on his cell phone.
Einstein cuts in to say that a man who's “smoking through a hole in his neck” would probably have a hard time talking to anyone.
Anyway, a series of tests on Mulder ensues, and Scully even sequences his DNA to check for alien DNA. There is no alien DNA, but there are certain abnormalities. Blah-blah-blah, immune system being turned off through manipulation of his DNA. This is something that could have been done to him as a child, through immunizations, but somehow triggered now.
Miller jumps in to suggest that the man at Mulder's house wasn't using chloroform, he was triggering whatever was in Mulder's DNA. Mulder starts to put together that Svetta's alien DNA wasn't about them putting something into Svetta, it was about them taking something out. What if everyone who was ever vaccinated has these genetic bombs that are waiting to go off, with certain people being altered to remove the threat.
All of this is just mumbo-jumbo to get to the point that Scully needs to find a way to reactivate Mulder's immune system. Einstein says that they would need a donor who was a genetic match. Scully says that Mulder's mother died six years earlier.
“Does he have any siblings?” Einstein asks.
“That's a loaded question,” Scully comments. “But it's not an option.”
Scully pauses. Of course they have a kid.
Mulder doesn't want to put William in danger That could be exactly what CSM was trying to do when he attacked Mulder. He'd rather die than put William back in CSM's sights. Scully isn't convinced that this is an issue. She thinks that Mulder was delirious when he saw CSM. He's dead. Reaching out to William might not be the threat that it once was.
Mulder points out that Svetta an Tad might think otherwise, since they're both missing or dead.
While they debate that issue, Einstein points out that if this is a widespread issue, with specific people being given immunity, there is obviously a threat for a large-scale attack here. If everyone in the country were suddenly to have their immunizations turn on them, they'd be dealing with countless types of outbreaks, all at the same time. It would be an apocalyptic event.
“For what purpose?” Miller asks.
“So that he can rule over the survivors,” Mulder explains.
“The cigarette smoking dead guy?” Miller asks, not entirely following.
And so this becomes the finale. Scully is on a search to find William and get a sample of his blood that could be used to cure Mulder. She discovers that William was adopted by a family named the Van De Kamps, but both parents fell ill soon after. Though both recovered, it wasn't until after they were forced to give up the child that they'd just adopted.
Suddenly, Scully's dream of William's adopted family is shattered. She is terrified.
Her search continues. She finds a social worker who handled William after the Van De Kamps gave him up. The woman says that the baby was nearly adopted by another family, but an FBI agent discovered that the couple wasn't actually married and their identities were faked. The child was in danger, so the agent managed to work out a sort of witness protection-type adoption for the baby. The circumstances were far from typical.
Scully asks the name of the agent who helped William survive. The social worker tells her, “Monica Reyes.”
Scully breathes a sigh of relief. She tracks down Reyes and the two talk. Reyes says that going to William would be incredibly dangerous. There are still people who would love to get their hands on him. Scully says that she needs this. She doesn't need to see him personally, but she needs his help and... she needs to know that he's okay.
Reyes reluctantly agrees to help, but she will meet with the adopted family, not Scully. Scully agrees to the terms, and waits for Monica to contact her.
While this is happening, Miller and Einstein are tasked with finding out what happened to Tad O'Malley. The investigation leads them to a big chase of some sort and a revelation about the apocalyptic plans of a mysterious group of people who have been faking alien abductions, etc... basically, it's like a season 1 Mulder/Scully investigation.
Scully returns to Mulder's side while he continues to deteriorate. She's trying her best to help him, but there's nothing that she can do. Finally, at the last minute, Reyes arrives with a sample of William's blood, as well as an envelope. In the envelope, there is a letter from William, telling his birth parents that he is okay and that he has had a good life, with a family that loves him. He knows that they didn't have a choice in giving him up, and he knows that they love him. He loves them too. He tells them to stay safe.
There is also a picture in the envelope. Scully pulls it out and looks at a picture of a teenaged William, with his adopted family. She immediately gasps, recognizing the people who have raised William. It's her brother, Charlie. William has been with family this whole time. He wasn't estraned from the family because of a falling out, he was estranged because he had taken on the task of protecting Dana's child.
She finally has closer, not only in regards to William, but in regards to her brother as well.
The blood saves Mulder, but Miller and Einstein warn Mulder an Scully that the potential for the apocalypse outbreak is still a very real threat. They don't have the answers they need to stop it yet.
Mulder tells them that they will find the answers. The truth is out there.
Scully rolls her eyes.