What happened to Samantha Mulder?

In the series finale Jeffrey spender testified at Mulders trial that after she was returned from her abduction from the Mulder house in the 70's she was sent to the Spender household where she and Jeffrey grew up together until she died in 1987. Given that the series didn't start til 1993, she was dead all along. For me, personally, this was a huge letdown. Mulder also admits Samantha is dead in I Want To Believe.

Yes, but nowhere does it specify how she actually died. There's all the preamble about her time on the base, running away, etc - but then she just 'disappeared' again without any real explanation and Mulder finds her soul cavorting around with a bunch of other child ghosts and gets his closure by believing she's dead and 'in a better place'. I always assumed that the fact she was found together with a bunch of other dead kids suggested it was the burial ground of a child serial killer and that she had been one of the victims after running off from the air base.

Ever heard of a “walk in” ? Yeah, me either until the season 7 episode "Sein Und Zeit", and the following episode "Closure".

Spoilers to follow.

Samantha Mulder was taken by the Syndicate. She was experimented on for years, her DNA taken and used to create the subsequent clones we saw throughout the series.

We learn in the episode "Closure" from a journal discovered by Mulder that in 1979, after being experimented on for six years at an army base in California, Samantha worked up the courage to escape.

Sadly, she didn’t make it very far and was picked up by two officers who took her to a hospital. Scully was the one who found the police report of a girl matching Samantha’s description being admitted to the hospital. The agents met the nurse who attended to the teenage runaway. The nurse said the girl seemed very sad and at one point the nurse had a vision of this girl dead. (This is an important plot point from the previous episode in which parents had visions of their children being dead right before they mysteriously disappeared.)

While in the hospital the Syndicate tracked down Samantha (the nurse said she remembered the one man whom she asked to put out his cigarette); they were there to take Samantha back to her prison. But, when they went into her room she was gone. Disappeared without a trace.

So what do we learn? Two parents of missing children tell Mulder about “Walk ins.” A type of entity that rescues children doomed to suffer a terrible fate and whisks them off to a type of ethereal realm where they can live forever.

I was always slightly underwhelmed with the big reveal of Samantha’s ultimate fate. It seemed so far from what was always believed happened to her.

It seems these Walk Ins would give the parents a vision of what was to befall their child. Almost like they’re saying, “Look this is what’s going to happen so instead we’re taking your kid to a type of heaven where they can live forever.” So Samantha was ultimately saved from her fate by Walk Ins.

As for the burial ground, those were children that were murdered by Ed Truelove. He had set his sights on a little girl named Amber. She was going to be his next victim but she was saved from this fate by the Walk ins. The other ghostly children seen by Mulder when briefly reuniting with his sister are assumed to all be children taken by Walk ins. Saved by them from experiencing a horrible fate.