The story opens with a view of the Earth from space, as Special Agent Dana Scully narrates a brief history of  life on Earth. The poetic tome details the history of the many cycles of life and mass extinction that the Earth has borne witness to. From the first single celled organism to Apollo 11, she relates the amazing development of that most precious of gifts, life. Acknowledging that no one can say for certain what or who ignited the original spark and the previous record of catastrophism, the question is put: "Will we pass as those before us into oblivion? Or is there a plan or purpose to our existence?"

The scene dissolves into a sandy beach, and a group of  Africans are excitedly scurrying around something in the sand ...

... finishing her own hanging question, Scully asks "Or will the secret be revealed through a sign, a symbol, a revelation?"

We then shift to the same sandy beach, now revealed as the Ivory Coast in Western Africa. Obviously we now see that the men are part of an excavation of some kind being led by an African scientist. Overhearing the excited cries of his workers he rushes to the site and extracts the strange artifact, which has odd writing or symbols all over it.

Back at his office at a local university, the scientist pulls a similar artifact from a locked cabinet and holds them close together. Just as we note that the broken pieces match along one side, they suddenly shoot out of his hands across the room, imbedding themselves in a book on the shelf. As the startled scientist pulls the book from the shelf, we realize just what book it has cut into ..

Pulling the now fused single piece from his Bible, the scientist sets it on a table where it promptly begins to rotate ...

Grabbing the artifact and wrapping it in a blanket, the panic stricken scientist rushes to his phone as we pan to the now discarded Bible and see that the artifact has cut into a very specific passage from the book of Genesis ...

The scene then shifts to the American University in Washington, DC, where our scientist is overheard asking for directions to the offices of a Dr. Sandoz. As he does so, he is watched by a man from a second story window. The man makes his way through a laboratory filled with monkeys and waits at the door for our scientist. They meet and the scientist introduces himself in a heavy African accent as Solomon Merkmallen. He assumes the man meeting him at the door to the lab is Dr. Sandoz. Merkmallen is obviously a bit concerned as the man he presumes is Dr. Sandoz does not seem to know certain details he should. As soon as he pulls the artifact from his briefcase, the monkeys become highly agitated. Merkmallen relates that he has come to demonstrate to Dr. Sandoz it's "Magic." When the mock Dr. Sandoz asks him if he has had any luck reading the symbols on the artifact, Merkmallen realizes that the man he is with is not Dr. Sandoz. Suddenly, Merkmallen is attacked. Shortly after, the real Dr. Sandoz returns to his lab and discovers not only the empty blanket and the missing artifact, but Merkmallen's bludgeoned body. Recognizing he'll be blamed for the murder, Sandoz flees.

The next day agents Mulder and Scully are being briefed on the case by Assistant Director Skinner. Skinner tells them that the body is missing but due to the amount of blood it assumed Merkmallen was murdered. Dr. Sandoz is the prime suspect. Mulder knows of both men and that they shared a belief in a theory called "Panspermia," the idea that life here originated off planet, a prime candidate being Mars in it's more hospitable past.

They question whether this shared theory may have had something to do with his death. Skinner tells them about the artifact and gives them a rubbing of it, informing them that Dr. Merkmallen "... claimed that it contained a message, not only of his Mars theories but the very meaning of human existence." Scully is of course unimpressed, but Mulder points out that the theories have been published in some science journals and that Sandoz had found a similar artifact.

As Mulder examines the rubbing closely for the first time, he is overcome by a high pitched noise and feels faint. Scully is concerned.

Back at the American University campus, Mulder and Scully examine the crime scene and are confronted by Dr. Barnes, the head of the biology department. We quickly realize that Barnes is the same man who impersonated Dr. Sandoz and killed Merkmallen. Barnes is harsh in his assessment of Sandoz, claiming he is capable of almost anything to advance his theories and calling him a "Pseudo scientist. Beyond embarrassment." He mentions the artifact and insists that it cannot be found, implying it is a fabrication. When Scully pulls the rubbing out and asks if it the same artifact, Mulder swoons again and staggers from the room.

Confronted by Scully, he tells her that he thinks the rubbing is the source of his discomfort.

Act 2 begins with Scully and another agent briefing Mulder concerning the rubbing. The other agent is fascinated by the effect the rubbing is having on Mulder. Scully asserts, with the other agents support, that the rubbing is fake because while the letters on it are Navaho, they make no literal sense, just random letters. Considering it was found in Africa, the case for it's authenticity is further weakened.

He goes on to explain that the artifact is laid out as a "Magic Square," a geometric puzzle that God himself instructed Adam to use. God then handed down the secret of their use to "all the saints, prophets and wise men as a way of trapping and storing magical powers to the person whose name or numerical correlative exercises that power."

Mulder is intrigued, but Scully shows him an article written by Barnes (which Scully describes as "brutal") accusing Sandoz of faking his work on the previous artifact. It seems that Barnes is something of a professional debunker, attacking anything in the least mystical or paranormal appearing in the press.

As they continue to discuss the artifacts authenticity, the other agent places the rubbing back on the overhead and Mulder is overcome again. Scully insists that he see a doctor, but Mulder refuses. He then tells her that he had a "sense," brought on by the rubbing, that Barnes killed Dr. Merkmallen. Scully of course is skeptical, but Mulder offers to show her where the body is hidden.

They go to Sandoz's house and Mulder discovers that Sandoz has made many trips to northern Mexico -- Navaho country. Scully discovers a picture on the wall of Sandoz with Albert Hostien, a World War 2 Navaho code talker who had helped them decipher secret government UFO documents written in Navaho code on an earlier episode, "Anasasi." Mulder surmises that he was helping Sandoz decipher the verses on the artifact, Scully that he was helping to write them. Mulder than shows her where the dismembered body of Merkmallen has been stuffed in the trash compactor.

Back at headquarters, Mulder and Scully brief Skinner on the status of the case. They inform him that parts of Merkmallen's body were missing -- the parts that would retain tell-tale signs of radiation exposure. Skinner is skeptical that it came from the artifact, but Scully had subjected the body to further tests which reveal it was exposed to CGR, "Cosmic Galactic Radiation," which is found only outside the solar system. Mulder then has another episode and accuses Skinner of secretly putting someone else on the case. Scully ushers him out, but we see that Skinner has secretly videotaped their conversation, then we see for who. He gives the tape to Alex Krycheck, an assassin for the "Consortium" (which represents Majestic 12 in the shows mythology) who had compromised Skinner in an earlier episode.

Act 3 begins with Scully arriving at a hospital in New Mexico just as Albert Hostien is wheeled past on a gurney. Scully goes to his room and finds another rubbing. On the back is written a translation of the same bible verse that we saw in the first act from the pierced bible.

She is confronted by a nurse and inquires as to Hostien's condition. The nurse tells her he is dying of cancer.

Back at the American University, Mulder sneaks into the office of Dr. Barnes. Mulder hides in the lab when Barnes returns, but Barnes notices something amiss and checks the lab. Barnes does not find him but Mulder is stricken with the most intense episode yet. Barnes then makes his way to the roof of the building with Mulder attempting to follow despite his increasing disorientation. Mulder tries to follow him up a stairwell but collapses as the pain becomes too great.

Back at the hospital Scully spots Dr. Sandoz trying to visit Albert Hostien. She chases him up a stairwell and eventually catches him. She tells him she needs answers.

Back at the University, Alex Krychek finds Mulder in the stairwell and ignores him. He proceeds to the rooftop where he meets with Barnes. Barnes doesn't know him but Krychek tells they are "Destined to be great friends." He then produces the video tape from Skinners office.

Back at the hospital Sandoz tells Scully that the pieces found by himself and Merkmallen had been translated into the Bible verse on the rubbing. He argues that extraterrestrials are the true authors of the bible. As proof, he produces yet another piece of the object and insists it will hold the key to the meaning of the other translations, even though so far Hostien had only found random letters. As Scully is digesting this, the new piece begins to rotate, faster and faster, until the shaken Scully slaps her hand down on it.

The scene shifts to Mulder's apartment where we find him in bed. We see there is someone else in the room with him. The phone rings and it is answered by Diana Fowley, Mulder's former partner on the X-files and now an operative for the Smoking Man, a member of the consortium and the shows chief villain. Scully tells him about the bible verse translation and they argue about the authenticity of the artifact, although Scully resistance is weakening. Mulder is certain that the artifact is proof that mankind was created by aliens. Fowley then takes the phone and makes a call out of Mulder's ear shot. She does not know what is wrong with Mulder but promises the person on the other end of the phone that she will stay until she finds out.

We then cut to a briefing of some kind, possibly in the Pentagon, and only barely overhear the ongoing conversation...

"... final preparations for mass destruction on a scale that can only be imagined."

"Well, what can we do to stop them?"

"There appears to be nothing we can do to prevent it."

"It becomes a question of managing the crisis. Otherwise we face annihilation ourselves."

As all this goes on, we pan around to see the recipient of Fowley's phone call -- the Smoking Man.

The final act opens with Scully again musing on the subject of life and death, questioning who lit the eternal flame of life on Earth and if it was part of the plan from the beginning of the universe 10 billion years ago. Is it destined to go out? And who decides if it is? As we listen, Albert Hostien is brought to an Indian healing tent. Modern medicine has done all it can, now they will try spiritual healing. Scully receives a call from Skinner and tells him she is with Dr. Sandoz in New Mexico. Skinner tells her that Mulder is in a Washington hospital in serious condition and for her to return as soon as possible. Sandoz pleads with her not reveal where he is until the last artifact is translated.

When she arrives at the hospital she is shocked to discover that Mulder is in the psychiatric unit. Skinner takes her to a video observation room where we can see that Mulder is pacing a padded cell, ranting. Fowley is there as well. The doctors have no idea what is wrong, but explain that while he should be in a barbiturate coma, he is instead very violent and has brain activity in areas never seen before.

Fowley begins to question Scully on the case and the rubbing. Skinner interjects that Scully has found ample proof that the rubbing is fake. Pointing out that she never sent him that report, Scully realizes they are both lying to her and stomps out. She goes to Mulder's office to search for bugs and finds one in the smoke detector. The phone rings. It is Sandoz from New Mexico. He has finally deduced what the "random numbers" on the last artifact are. They are coordinates for gene clusters on the human genome. Realizing this may be proof that humanity was created by extraterrestrials, Scully is stunned. Sandoz says they need more pieces to prove the hypothesis. Before she can respond, she hears a gunshot over the phone line. Krychek has killed Sandoz.

The scene switches back to the sandy beaches of the Ivory Coast 36 hours later. Scully is guided to a spot that most of the workers are afraid to go near. In the sand she finds another washed up piece of the artifact, this one much larger ...

Suddenly she realizes it is not a piece, but the edge of a much larger, partially buried --

-- Alien spacecraft!