Good news is it wasn't really him. Bad news is it was actually Mulder and Scully's son, William, who was shot by CSM directly in his face, after William shapeshifted himself into Mulder. However, a quick plot twist had Scully revealing to Mulder that William was actually not their child. "William was an experiment, Mulder," Scully explained. "He was an idea. Born in a laboratory. I carried him, and I bore him. But I was never a mother to him." Mulder was devastated by the news, as he questioned, "What am I now if I'm not a father?" Scully then dropped another bombshell revelation. "You are a father," she told Mulder as she grabbed his hand and placed it on her belly. No, this is not a drill. 54-year-old Dana Scully is pregnant! With Mulder's child. We hope.
But before the happy ending, came some shocking deaths. One of which was possibly a beloved character. Walter Skinner stayed behind to take aim at CSM and Monica Reyes, the latter of whom he actually killed. Unfortunately, CSM managed to grab ahold of the car wheel, presumably smashing the vehicle into Skinner. But whether or not Skinner really is dead is up to creator Chris Carter and a potential 12th season?
One death that fans were sure of, and satisfied by, was the death of Mulder's longtime arch-nemesis, Cigarette Smoking Man. After CSM shot William, whom he thought was Mulder, the real Mulder stood up and shot CMS. Multiple times.
Overall, fans generally seemed to like the finale, as they tweeted: "Me, now that #TheXFiles has ended, yet again:" and "I legit didn’t think that #TheXFiles could still shock the crap out of me again... but here I am, more shocked than ever"
And while it's uncertain whether or not The X-Files will return for a 12th season, if it does, at least we know one character is likely to return. Spoiler alert: William survived!