1. Agent Scully is assigned to Agent Mulder to debunk his work in the X-files
2. They both start to uncover an alien conspiracy to colonize the planet
3. The conspirators recognize Agent Scully as a threat and abduct her in a "staged" alien abduction, as well as other women, and give her an implant which she removes and therefore gives her an incurable cancer.
4. The Cigarette Smoking Man gives Agent Mulder the cure.
5. Mulder and Scully then find the conspiracy involving black oil, which contains an alien virus that controls humans and turns them into aliens.
6. Mulder and Scully fall in love.
7. Mulder is abducted by aliens and we learn Scully is pregnant, but it is not clear on the nature of the pregnancy.
8. John Doggett is assigned to help find mulder but is unsuccessful but becomes Scully's new X-Files partner.
9. Mulder is returned, barely alive, but recovers, and is unsure how Scully is pregnant.
10. Scully has her child, William, and Monica Reyes enters as a new X-files member agent.
11. Mulder goes into hiding and no one knows why but meanwhile William is a miracle child for the human race with abilities that are able to fight the aliens and that puts him in danger.
12. Scully is forced to give up William to an anonymous family to protect him.
13. Scully, Doggett, and Reyes uncover the conspiracy of super soliders, humans replaced by aliens who cannot be killed unless by a rare metal called magnetite which is only found in the new mexico desert.
14. Scully, Reyes, Doggett, and Skinner find out that Mulder has been put on military arrest for "killing" a super solider and they try to save him. Scully and Mulder are reunited and we learn William is Mulder's child.Skinner tries to defend Mulder in a rigged military court of law. Old contacts testify. Mulder is found guilty and is to be given death by lethal injection. Scully, Reyes, Doggett, and Skinner break out Mulder. Scully and Mulder go to New Mexico onyl to find the Cigarette Smoking Man alive and knows Mulder has found the truth and that he hasnt told Scully. We then find out the truth is that the alien colonization is to begin on December 22, 2012. Mulder and Scully then go into hiding together, and the last scene is them in bed together.
this is a very VERY concise summary. there were like 280 something episodes. this basically outlines the mythology episodes which dealt with the alien conspiracy but the rest were "monster of the week" with more important happenings.
if you go to en.wikipedia.org then type in X-Files you can read the entire summary of each season.