Spoiler alert: This recap contains plot details for the second episode of “The X-Files.”

A marked improvement on the disappointing premiere, Monday’s second episode of “The X-Files” is a welcome return to the kind of standalone stories that fans have been waiting for. Why show creator Chris Carter chose to relaunch the series with a muddled mythology tale rather than this fresh one-shot is a mystery that not even Mulder and Scully could solve.

Titled “Founder’s Mutation,” the episode begins in a high-tech biochemical company called Nugenics Technology, where Dr. Sonny Sanjay is experiencing painful migraines that quickly become full-blown auditory hallucinations. Run by a mysterious scientist named Augustus Goldman, Nugenics Technology is apparently involved with cutting edge stem cell research.

Locking himself in a computer lab, Dr. Sanjay scribbles something on his palm moments before skewering himself through the ear with a letter opener to drown out a piercing sound that only he can hear.

This gripping opening sequence recalls a memorable 1995 episode titled “Soft Light,” about a troubled physicist whose experiments in dark matter led to otherworldly occurrences.

Back on the case, Mulder and Scully investigate Sanjay’s suspicious death. Before they can tag his hard drive as evidence, the Department of Defense steps in and prevents it. Whatever work Nugenics is doing is highly classified.

Luckily, Mulder is “old school,” so he steals Sanjay’s cell phone and discovers that he was calling someone named Gupta virtually every night. Genius that she is, Scully helpfully mentions that Gupta is a Marathi word meaning “secret.”

“How did you know that?” Mulder asks in amazement.

“I’m old school, too,” she wryly comments. “Pre-Google.”

Unlike the dramatically inert first episode, the chemistry here between Mulder and Scully seems much closer to the playful banter we’re used to from the good old days.

At a Washington D.C. bar, Mulder meets with Gupta and discovers that Sanjay was living a “second life,” complete with a secret apartment. Meanwhile, Scully performs a wonderfully gory autopsy on Sanjay, slowly withdrawing the bloody letter opener from his ear in gruesome closeup. Now this is the Scully we’ve missed!

In the FBI morgue, Scully shows Mulder the hidden message that Sanjay scribbled on his palm before killing himself. It cryptically reads: “Founder’s Mutation.”

Later that night, Mulder and Scully enter Sanjay’s secret apartment and search it, their flashlights gleaming in the darkness. Why don’t they simply turn on the lights, you ask? Because flashlight beams are one of the hallmarks of the original series, naturally!

Just as they discover a wall covered in weird photos of deformed children, Mulder is struck by the same kind of high-frequency sound attack that led Sanjay to kill himself.

The next day in Skinner’s office, Mulder and Scully are ordered by the Department of Defense to end their investigation into Sanjay’s death. But Skinner, awesome boss that he is, hints that he can buy them a few extra days to continue their pursuit of the truth.

“Welcome back, you two,” he adds, before sending them on their way. Gotta love that Skinner!

Using her connections at Our Lady of Sorrows, Scully wrangles a meeting with the enigmatic Augustus Goldman, who’s been making large financial donations to the hospital. However, a strange encounter with a young pregnant woman named Agnes triggers an emotional confrontation between Mulder and Scully about their son, William, who they put up for adoption years ago.

“He’d be 15 years old now, and I’ve missed every single year of his life,” Scully whispers, clearly feeling the loss. But Mulder stoically claims to have put the pain behind him.

The dream sequence that follows, where Scully fantasizes about what her life might’ve been like if she hadn’t given William up for adoption, allows Gillian Anderson to do some of the best work in the series so far. It’s powerful stuff, climaxing in a chilling image of her helpless son slowly transforming into an alien.

After visiting with Augustus Goldman and the tragically deformed children under his medical care, Mulder and Scully learn that Agnes, the young pregnant woman they met earlier, has been killed by a hit and run driver. Worst of all, her unborn child has been surgically removed and stolen.

Suspecting that Goldman is experimenting on children, Mulder and Scully interview his ex-wife Jackie, who’s been locked away in a mental institution for the past 17 years. According to Jackie, Goldman genetically altered their daughter Molly, and would’ve done the same thing to their unborn son had she not run away while still pregnant. Following a devastating car accident, Jackie cut open her own belly and removed her son, who she believes was trying to communicate with her using high-frequency audio waves.

In short order, Mulder and Scully discover that Goldman’s son is still alive and may be responsible for Sanjay’s death. Apparently, his name is Kyle and he’s been secretly working at Nugenics Technology as a janitor.

Tracking the teenage Kyle to his adoptive home, Mulder and Scully take him into custody, but not before Kyle briefly cripples Mulder with another blast of sonic energy.

Though it doesn’t seem like the best plan they’ve ever come up with, Mulder and Scully decide to take Kyle to visit Goldman in the hopes that he’ll… what? See the error of his ways? Introduce Kyle to his long-lost sister? Gain some sort of closure? It’s more or less a Hail Mary play on the part of our FBI heroes at this point.

Of course, things go terribly wrong, and before you can say “Chronicle,” the reunited siblings are using their psychic superpowers to toss Mulder and Scully around like rag-dolls while simultaneously crushing Goldman’s brain like an egg. When the two agents finally regain consciousness, they learn that Kyle and Molly have escaped.

The episode ends with another dream sequence, but this time from a different perspective. Now we see Mulder and William, father and son, watching Stanley Kubrick’s “2001: A Space Odyssey” together. This is Mulder’s vision of what his life might’ve been like if he’d been allowed to raise his child. Yet after an idyllic image of Mulder and William firing a home made rocket into the sky, the dream turns into a nightmare that recalls the alien abduction of his sister Samantha.

The final shot is of Mulder, alone, staring longingly at William’s baby photo. Clearly, he hasn’t put the pain behind him after all.