The X-Files Miniseries Finale
Agent Miller (Robbie Amell) and Scully (Gillian Anderson) try to save Mulder in the finale of "The X-Files" miniseries. Fox

"The X-Files" miniseries finale came to an end with a bang as a disease known as the Spartan Virus started to break out all around the world. The cure to saving the world lies within Scully (Gillian Anderson) and she has to move quick to save lives, including Mulder's (David Duchovny). However, it wouldn't be an "X-Files" finale if it didn't come to an end with a shocking cliffhanger. Here are the top 11 moments from episode 6, titled "My Struggle II."

1. Scully's Opening

Episode 1, “My Struggle” started with a monologue by Mulder gettig the audience up to speed on where "The X-Files" left off. In “My Struggle II,” Scully has her own monologue where she talks to the audience about the new government conspiracy where alien technology was being used on humans and was hidden for years. The opening took viewers on a quick journey throughout the show up to this latest episode. Scully also reveals she has found traces of alien DNA within her.

2. Ted O'Malley Back Online

Tad O’Malley (Joel McHale) returns to the internet and in a video he tells the world that there is alien DNA inside of every person, put there without their knowledge. O'Malley was off the air for six weeks, but had to return to let the world know that trouble was on the way. The web series host kept the audience informed on what was going on throughout the finale.

3. Mulder's Disappearance

O’Malley calls Mulder’s office and Scully answers the phone. O’Malley is at Mulder’s home, which has been trashed and the agent is nowhere to be found. Mulder also isn’t answering his cell phone and Scully fears what he learned from O’Malley has got him worked up. A beaten-up Mulder is then shown in a car, ignoring phone calls and speeding off somewhere. Agents Einstein (Lauren Ambrose) and Miller (Robbie Amell) arrive to assist Scully.

4. A Global Contagion

Scully suggests something might have been put in each person through vaccines. O’Malley reveals on his show that soon people’s immune systems will start shutting down as different diseases and illnesses start to make people sick. As the military starts get infected, Scully and Einstein begin to realize it’s an actual possibility and learn the event will be global.

5. Monica Reyes Returns

Scully gets a call from someone while at the hospital that claims she knows why people are getting sick. The woman turns out to be Scully’s old partner, Monica Reyes (Annabeth Gish). When Scully meets with Monica, she tells Scully that the Cigarette Smoking Man (William B. Davis) is still alive. The Cigarette Smoking Man is the one who set everything in motion and he got Monica to work for him by offering her immunity from the disease he spread around the planet.

6. Scully Is Immortal…Kind Of

Monica also tells Scully that she’s been selected to be one of the chosen few who will survive the outbreaks. Scully is worried about Mulder, but Monica assures her that the Cigarette Smoking Man loves Mulder and sent a man to retrieve him. She lets Scully know that the disease is called the Spartan Virus, which takes out people's immune systems and allows them to get deathly sick.

7. Mulder Reunites With Cigarette Smoking Man

Mulder gets into a fight with the man sent to retrieve him at his home. After a long battle, Mulder beats the man and finds out he was sent by Cigarette Smoking Man. Mulder finds the Cigarette Smoking Man, who tries to convince Mulder to join him and the chosen. If he doesn’t, Mulder will die of some sort of sickness. The Cigarette Smoking Man says humans have been killing the planet and what’s happening is inevitable, but he just sped up the process to start a new world with the people he's given the cure to. Mulder refuses to play ball and begins to get very sick.

X-Files Top Finale Moments
Cigarette Smoking Man (William B. Davis, left) and Mulder (David Duchovny, right) come face-to-face with one another for the first time in 14 years in the finale of "The X-Files" miniseries. Fox

8. Miller Saves Mulder

Miller was able to use Mulder’s computer to track his cell phone, which leads him to Cigarette Smoking Man. Miller arrives, grabs the very sick Mulder and starts to take him to his car to get him to help. The Cigarette Man doesn’t try to stop them because he says there’s nothing they can do to change things. Before Miller leaves he turns to Cigarette Smoking Man and asks who he is. The man doesn't answer, but tells him to tell Mulder he said goodbye before he dies.

9. Scully’s Cure

Scully finds a vaccine to the Spartan Virus using her DNA. The alien DNA inside of her prevented her from getting sick, while everyone else ended up getting sick because they don’t have alien DNA. Einstein starts to get really sick and Scully hooks her up to an IV with the vaccine hoping to get her feeling better to help make more of the vaccine.

10. Scully Needs William To Save Mulder

After taking a car and driving on sidewalks to get to Miller and Mulder, Scully finally finds them on a bridge. When she sees Mulder she realizes he’s even sicker than she thought and he’ll need more than an IV to be cured. She tells Miller that Mulder needs stem cells from their son William, but neither of them know where he is.

11. Aliens, the Chosen Ones or William?

Just as Scully says she doesn’t know where William is, an ARV ship appears overhead and drops a light beam down on Scully. Everyone on the bridge looks up at the ship in amazement and the episode comes to an end with Miller and Scully looking right up into the light. Was it aliens? Her son? Or the Cigarette Smoking Man’s chosen? We’ll have to wait until the next chapter to find out.