Ignoring the restrictions and news reports about toxic nerve gas - an attempt by special governmental agents to prevent the public from discovering the alien visitation, Roy frantically drives in a rented station wagon [with Wyoming plates] to the town Moorcroft, WY while again fiddling with road maps, as the radio broadcasts warnings of more road closures:

...and thousands of others are homeless. The United States Army Material Command has issued these new area restrictions: All roadways north of Crowheart on Interstate 25, all roads leading into the Grand Tetons west of Meeteeste, all multi-lane undivided full traffic interchanges, railroad, local and historic stage roads south of Cody...

Roy mutters to himself about the indecipherable map markings: ("Why aren't there any fat lines instead of these thin ones?"), just avoiding a collision with vehicles on a two-lane road streaming away from the quarantined area. He is directed toward a rural train depot where thousands are departing in a chaotic, crowded scene under Army control. Street vendors take advantage of the crisis by selling "an early-warning system." They are hawking gas masks and live birds in cages to detect the GM nerve gas. Roy notices how desperate people are pushing each other, and handing their luggage up to train windows.

Roy hears his name called out by Jillian through the deafening din of the train depot, as she is boarding one of the freight cars. Instinctively, they have both come for the same reasons - the two locate each other amidst the crowd and rush to each other's comfort. After driving out of town together, Roy turns off the main highway and drives through fence after fence and open fields because of multiple road closures: "Look, the only way we're gonna get back in there is to go cross-country...We gotta break through the fence."

Jillian shares some of the details of the search for her son after he disappeared - the river was dragged by the police, and they also looked inside backyard refrigerators. She also remembers one of their questions:

They asked me if I'd seen any strangers in the neighborhood.

And then, they both see the familiar shape at the same instant - Devils Tower. It looms up from behind a hillside as the camera makes a slow pan upward.

Jillian: I don't believe it's real. I don't believe it's real.
Roy: It's real. Let's get down there. Get some gas and get down in there.

As they drive further toward the monument, they encounter bodies of dead animals - three dead horses and then three dead cattle. Jillian checks to see that the caged birds are still alive. Roy is confident that it's all a hoax - a simulated nerve-gas scare:

Look, I guarantee you, that this whole thing is a put-on.

Wordlessly however, after an exchange of glances, they both don gas masks and roll up the car windows. They pass more bodies of sheep littering the side of the road. After rounding a curve, they are blocked by vehicles peopled by white-uniformed men in gas masks, and Roy is belligerent: "The only bad air around here is you guys fartin' around." The two unwelcome humans, Roy and Jill are separated into two different vehicles and firmly taken into custody. He is questioned in a small holding room [in the decontamination camp] by Laughlin and Lacombe:

Laughlin: We need answers from you that are honest, direct, and to the point.
Roy: Where's Jillian?
Laughlin: (translating for Lacombe) Do you realize the danger that you and your friend have risked? By coming here, you've exposed yourself to toxic gas.
Roy: Well, I'm alive. We're talking.
Laughlin: This is true, Mr. Neary. But if the prevailing winds were blowing from the south instead of the north, this conversation would not be taking place.
Roy: There's nothing wrong with the air.
Laughlin: What makes you say that?
Roy: I just know. There's nothing wrong with it.
Lacombe: Go outside and make me a liar.
Roy: Uh, look, I want to talk to the man in charge.
Laughlin: Mr. Lacombe is the highest authority.
Roy: He isn't even an American.

Roy is asked if he has any physical symptoms: a persistent ringing in his ears, any headaches, migraines, an irritation in his eyes and sinuses, hives or allergies, a burning on his face and body. He answers affirmatively to most of the questions, but becomes exasperated with them after being shown a drawing of Devils Tower: "Yeah, I got one just like it in my living room. Who are you people?" His question remains unanswered. Their final question is all revealing: "Have you recently had a close encounter - a close encounter with something very unusual?" He again asks: "Who are you people?"

As he is shown about a dozen snapshots of individuals who have also come on a pilgrimage to Devils Tower [prior 'chosen' witnesses of UFOs], he can identify only one who isn't a stranger - Jillian.

Laughlin: And the two of you felt compelled to be here?
Roy: Yeah, you might say that.
Laughlin (translating): But what did you expect to find?
Roy: An answer. That's not crazy, is it? (Laughlin and Lacombe speak to each other in French)...Hold it, hold it, hold it! Is that it? Is that all you're gonna ask me? Well, I got a couple of thousand, god-damn questions, you know. I wanna speak to someone in charge. I wanna lodge a complaint. You have no right to make people crazy...If this is just nerve gas, how come I know everything in such detail? I've never been here before. How come I know so much? (raising his voice) WHAT THE HELL IS GOING ON AROUND HERE?! WHO THE HELL ARE YOU PEOPLE?!

Wearing a gas mask and flanked by guards, Roy complains vehemently as he is led from the compound at the base of Devils Tower to a waiting transport helicopter filled with like souls: "I didn't come this far just to be taken on any bus ride home." As he anxiously looks around at other gas-masked faces inside the copter, he finds Jillian's familiar face.

The military leader of the project, Major Walsh reprimands Lacombe for disobeying proper evacuation procedures:

Walsh: You brought in twelve people to the decontamination camp instead of the evacuation center where they belong. I'd like to know why.
Lacombe (and Laughlin): Because this means something. These people have come from all over their country to a place they have been told will endanger their lives. Why?
Walsh: Because somebody could be trying to subvert this whole operation by sending in fanatics and cultists and Christ knows what all.
Lacombe (and Laughlin): (while showing sketches drawn of Devils Tower by all the captives) This is a small group of people who have shared a vision in common. Look. (He pulls up the shade to reveal the Tower in the window) It's still a mystery to me why they are here. Even they do not know why.

Taking a chance, Roy removes his gas mask because he doesn't accept the poison gas ruse. He encourages Jillian to follow his lead: "Listen, there's nothing wrong with the air around here. The Army is getting us out of here because they don't want any witnesses." One of the women obediently objects: "But if the Army doesn't want us here, then it's none of our business." A few more remove their masks - one comically jokes: "The air here is better than it is in Los Angeles." Roy encourages everyone to escape their captors: "How many of you people are for getting out of here?"

Back inside, Lacombe wants to discover why so many people inexplicably came together at Devils Tower:

Lacombe (and Laughlin): I believe that for every one of these anxious, anguished people who have come here this evening, there must be hundreds of others also touched by the implanted vision who never made it this far. It's simply because they never watched the television. Or perhaps they watched it, but never made the psychic connection.
Walsh: It's a coincidence. It's not scientific.
Lacombe: Listen to me, Major Walsh, it is an event sociological.

Roy, Jillian, and another man Larry Butler (Josef Sommer) decide to escape from the copter. At the same moment, in an artfully-composed image, Lacombe glances outside through a window (that reflects the image of Devils Tower), joyfully suppressing any word of alarm once he sees that the three escapees are running through the command post and toward the slopes of the mountainous area of the tower.

One of the Major Walsh's plans to keep people off the mountain is to dust the quarantined area with EZ-4 - "It's a sleep aerosol - same stuff that we use with the livestock. Comes out of Riot Control. They'll sleep for six hours and wake up with a hell of a headache, that's all." As Walsh walks away after ignoring Lacombe's request not to use riot control methods, Laughlin yells after him that the people he questioned were hypnotically compelled to travel there - they were mysteriously drawn there in their quest for something they couldn't fully comprehend:

We didn't choose this place. We didn't choose these people. THEY WERE INVITED! They belong here more than we.

Roy, Jill, and Larry climb up the steep incline on the side of Devils Tower. In a Spielberg scene that evokes Hitchcock's North by Northwest (1959), helicopters buzz by with loudspeakers blaring a warning: "The authority in this park has been superseded by the United States Government...You are entering a military reservation and subject to military law." Roy cautions about climbing up the steep face toward the top: "It's a three hundred foot drop straight down," and instead proposes taking a gradual incline trail to the right that leads to a box canyon. Jillian and Larry both realize their perspectives were inaccurate in their drawings:

Jillian: I never imagined that in my paintings. I only painted one side.
Larry: There was no canyon in the doodles that I made.
Roy: Next time, try sculpturing.

Ground troops search behind them on foot with "nothing to report at mid-station. It looks up ahead that there's thousands of places to hide. We're gonna need at least three times the men if you want this covered in one hour." The searchers are ordered "off the northern face" so that helicopters can begin dusting the area with the EZ-4 sleep aerosol. As night begins to fall, they press on and scramble for hiding places when another helicopter approaches. Larry falls behind and pauses to rest in the open, exhausted by the climb. The sleep-inducing helicopter, one with nightmarish sand, passes over him and releases a cloud of dust. Like so many other fallen birds, he quickly drifts off to sleep after inhaling the dust. Roy keeps encouraging Jillian: "Don't look back! Come on, come on!"

As they near their goal, they can see spot lights shining into the evening sky. After an exciting pursuit scene as they crawl and pull each other along (with outstretched hands) to avoid another spraying by the dusting helicopter, they emerge through a notch at the pinnacle of the tower. There, they are rewarded with the discovery of a colossal runway. The huge extinct volcano with its incredible mountain formation has been transformed into a secret landing site for UFOs. All of Roy's and Jillian's premonitions, obsessions, and implants now make clear sense.

The Final Close Encounter:

The film concludes with the climactic sequence at the Devils Tower National Monument. The extended scene is filmed with breathtaking special effects and a sense of awe and wonder. At the landing site where the UFO will touch down, the first maximum-publicity meeting and physical contact between the alien visitors [the unknown and imagined world] and scientists [the known and real world] will be experienced. A loudspeaker announcement prepares the scientific crew awaiting the aliens' visit:

Gentlemen, ladies, take your positions, please. This is not a drill. I repeat. This is not a drill. Could we have the lights in the arena down sixty percent, please? Sixty percent. I don't think we could ask for a more beautiful evening, do you? OK, watch the skies please. We now show uncorrelated targets approaching from the north northwest.

In the sky above them, streaking objects resembling comets whoosh through the blackness. Roy whispers expectantly to Jillian: "We're the only ones who know. The only ones." Three tiny, neon-lit scout ships appear with the tiny red orb following in their wake - they hover over the end of the runway. Audio analysis personnel ready themselves to communicate with the sparkling, illuminated objects at the rendezvous point. A giant electronic board covered with colored strips and a powerful synthesized musical keyboard have been constructed at the site. The Air Force scientists duplicate the electronic sounds that they have heard in transmissions, mixing them with light sequences (on colored strips) to communicate. The computer and audio specialists play the loud clear sounds of the five-note sequence after the signal: "Sunset":

Start with the tone. (Pinkish-red) - G
Up a full tone. (Orange) - A
Down a major third. (Purple) - F
Now drop an octave. (Yellow) - F (an octave lower)
Up a perfect fifth. (White) - C

[Best Animated Feature Oscar-winner Happy Feet (2006) directly referenced this scene in which the penguin population communicated with "aliens" (humans) by dance steps exchanged between the two, after the human's "space ship" (a helicopter) arrived and perched on a Devils Tower-type outcropping.]

French scientist Lacombe suggests that the organist play the sequence with an increased tempo and try different frequencies for the five notes or tones, to lure the friendly spacecraft to respond, as he marches out to the end of the runway. The three ships dance above the runway and respond with their own duplicate tones - they emit the musical sounds in the specific combination of five notes. And then they fly off, separating and soaring heavenward. Applause exuberantly erupts through the audience.

The show appears to be over - but it isn't. Lacombe looks into the skies, commenting on what's happening: "I don't know, but it is beautiful." A magnificent cloud formation erupts all around the Tower in the moonlight, creating a radiant halo. More colored flashing lights in the cloud cover signal the arrival of many more spacecraft. The squadron of neon shapes and lights encircles the entire area and buzzes the runway, causing panic and fear among the humans. One of the brilliant and bedazzling ships, looking like a galactic version of the Goodyear blimp, makes a slow, close pass over the base, drifting by and shining its underside of luminescent, sparkling colors.

Roy wishes to make his way down to the base itself, so he can experience the light show of spacecraft firsthand, but Jillian is not ready to join him:

Roy: Want to see better?
Jillian: I can see fine.
Roy: We can't stay here.
Jillian: I can.
Roy: Why?
Jillian: Because, Barry's not here. I'm just not ready.
Roy (impatiently): I can't stay here. I've got to get down there.
Jillian: I know. (They kiss quickly and impulsively)

Another loudspeaker announcement: "This is data control to all personnel: We monitor no biologic hazards. Range: Safety clear." Everything is very quiet until a deep rumbling, low-pitched vibration begins to build and increase in volume and intensity, suggesting the appearance of something awesome, incredulous, and frightening.

The appearance of multiple spacecraft is followed by an immense alien mother ship, a circular object double the size of Devils Tower itself, with hundreds of glittering, illuminated windows. Everyone shares the mass communal experience - they gaze with mouths agape up into the sky as the enormous vessel dwarfs the Tower and revolves and slowly descends toward them. It is staggeringly beautiful as it draws near for a landing. [In the lighted decorations under the Mothership, one can allegedly see an upside-down R2D2 from Star Wars, a shark image from Jaws, and other recognizable objects.] The light from the ship is so bright that dark glasses must be worn. The great space vessel touches down at the end of the runway. The loudspeaker presents another safety warning: "There is a safety hazard zone extending twenty-five meters from the ship. Special teams are exempt and should be aware of low gravity. Expect some dizziness and look out for static charge. All departments that are operational during this phase, signify by beeping twice."

One of the mission commanders directs other audio specialists to communicate with the craft by playing the five mystical notes: "If everything is ready here on the dark side of the moon, play the five tones." The speakers and flashing lights play the familiar tonal sequence toward the ship. The large ship answers with a deep, bass vibration played in coordination with flashing lights around the lower rim of the vessel. There is a back-and-forth musical duet as the conversational light/sound show-contact continues:

Give her six quavers, then pause.
She sent us four quavers, a group of five quavers, a group of four semi-quavers...
What are we saying to each other?
It seems they're trying to teach us a basic tonal vocabulary.
It's the first day of school, fellas.
Take everything from the lady. Follow her pattern note for note.

Jill is drawn forward and hurries toward the runway and the ship. One of the audio specialists realizes that they are actually communicating (or interlocked) in a joyful mood with the alien ship: "We have a translation interlock on their audio signal. We're taking over this conversation now."

After the notes of the ship slowly die out, a large cargo door in the belly of the ship slides open - a blinding, brilliant white light emanates from within. The panel slides down and becomes a ramp. From inside the ship and the ramp, uniformed figures emerge - the US Navy pilots missing for decades:

• Frank Taylor, Lieutenant J.G., United States Naval Reserve, 064199
• Harry Ward Craig, Captain United States Navy, 043431
• Matthew McMichael, Lieutenant, United States Naval Reserve, 0909411

As the long-missing military men step off the ramp, their names are checked off against lists of missing: "Records indicate Harry Ward Craig disappeared off Chicken Shoals, Flight 19."

- They haven't even aged. Einstein was right.
- Einstein was probably one of them.

Many other soldiers, as well as ordinary folks, are released from onboard the ship. They are checked off on an illuminated board of 'missing persons'. Jillian's small son, Barry, also appears on the ramp - he breaks into a run into his mother's arms.

Lacombe: Monsieur Neary, what do you want?
Roy: I just want to know that it's, it's really happening.

Barry describes his thrilling abduction during his reunion with Jillian:

Barry: I went into the air and I saw our house.
Jillian: I saw you going up in the air. Did you see me running after you?

Lacombe turns to Roy and tells him: "I envy you." The ramp opens up a second time and a small, frail, undeveloped, spindly, pale alien with big eyes gracefully debarks - the brilliantly over-exposed scenes cause the aliens to appear blurry. The vulnerable being with superior intelligence, a messianic figure of sorts, gestures with a message of love and peace to investigating scientists via sign language - he raises both his arms in a good-will gesture. Other small, childlike humanoid aliens, obviously harmless, emerge and stand on Earth's soil to face the humans. Having been cleared by Lacombe and Laughlin of official formalities, Roy is invited to join the red-uniformed team of "pilgrims" for a space journey in the alien ship:

Scientist: Mr. Neary, I'm told that we can count on your complete cooperation. What type of blood do you have?
Neary: I don't have the slightest idea.
Scientist: What is your date of birth?
Neary: Uh, December 4, 1944.
Scientist: Have you been inoculated against smallpox, diptheria - is there any history of liver disease in your family?

Roy Neary is last in the line of red-uniformed space travelers. One of the little aliens senses Roy's oneness with them, draws him out of the line and takes his hand. After being surrounded and 'adopted' by the beings, Roy is led up to the ramp. He briefly pauses and turns back at Earth with a look of calm on his face. Lacombe nods assurance and approval. Roy disappears into the brilliance of the Mother Ship.

One extra-terrestrial alien remains. The French UFO expert Lacombe gestures to the alien with the Zoltan Kodaly hand signals for the five-tone sequence (similar to Disney's "When You Wish Upon a Star" from Pinocchio (1940)). The alien responds, pleasingly, to the hand-to-hand communication with a repetition of the same signals. The extraterrestrial turns. After entering the giant spacecraft, the massive object lifts and gracefully heads starward. From his vantage point, Barry speaks a farewell: "Bye" - the film's final line of dialogue. There is an embellished chorus of the five notes, as the credits begin to play. The song "When You Wish Upon A Star" is also incorporated a few times in the closing music score.