TOKYO — The kaleidoscopic stands of Tokyo’s Olympic Stadium — a disordered mosaic of white and green and reddish-brown seats — were designed to evoke the sun-dappled floor of a Japanese forest.

Over the past three weeks, though, they have had another, useful effect: Squint your eyes, blur them just so, and it almost appears as if spectators are arrayed around the sweeping structure, as if the 68,000-seat stadium is not essentially empty, as if these are a normal Olympic Games.

Of course, they were not. On Sunday night in Tokyo, a stripped-down closing ceremony in Japan’s sprawling national stadium will bring these extraordinary Games to an end, concluding an Olympics that, in some sense, felt like an illusion — at times convincing and fully welcome, at others jarringly off-key.

Pushing forth in a pandemic, these Games were meant to be, as the International Olympic Committee president Thomas Bach said last year, “the light at the end of this dark tunnel the whole world is going through.” Yet they were often claustrophobic, cut off from society, with capacious venues across Tokyo repurposed into cloistered safe houses.

They were, in this way, paradoxical, uncanny and hard to wholly comprehend. They were a feat of organizational planning and execution, even amid arguments about whether they should be happening in the first place. They were stubbornly called Tokyo 2020, a retrograde name that reminded everyone of the meandering path traveled to this point. They were a made-for-television spectacle, stage-managed at times to the point of absurdity.

For athletes, these were an Olympics of survival, of resilience, of getting by and sometimes, in the end, being OK with falling short of a target. Yet even among medalists, there were feelings of ambivalence about being here, about enduring the alienating circumstances of one of the oddest Olympics in history.

“I can’t wait to get home,” the American sprinter Allyson Felix said after winning a bronze medal on Friday to become the most decorated female track athlete in Olympic history. “I’m counting the days, there are so few now.”

The coronavirus pandemic forced athletes to travel and perform here without the presence of friends or family, to say nothing of fans. They spent their time largely confined to their rooms, specially arranged buses and sports venues.

Though the lasting effects of the Olympics on Japan will be determined only in the weeks to come, early signs showed that the health protocols — the effort to cut off thousands of visitors from Tokyo residents — seemed to work, at least in the short term. At a news conference on Friday, Bach reported that 571,000 screening tests had been performed at the Olympics, returning a positivity rate of just 0.02 percent.

But the path to that point, the means of establishing what an I.O.C. spokesman called a “parallel world” inside the Games, has had an unmistakably estranging effect.

In the Olympic bubble, the competition sites — 38 in all — became eerie ghost ships. A surplus of volunteers manned stations that saw no foot traffic. Dance troupes performed in front of empty stands. Stadium announcers excitedly revved up nonexistent crowds. Events felt as if they could have been taking place almost anywhere — a sports hall in Stockholm, a convention center in Kansas City, a gymnasium in Dubai — so few were the distinguishing markers of place.

“If it had not been for the pandemic, this would go right up near the top of the best organized Olympics,” said the Olympic historian David Wallechinsky, who was attending his 19th Games.

The Olympics as a whole seemed like an oyster shell without a pearl.

The hollow feeling, on one hand, resulted from a relative deficit of once-in-a-generation standout performances in the most closely followed sports, and the handful of crowning achievements lacked the roar of a crowd.

Superstar athletes wilted under the city’s punishing sun, and established champions failed to live up to their own high standards.

Throughout, the motto “Citius, Altius, Fortius” — faster, higher, stronger — did not carry its old currency. Vulnerability, self-awareness and imperfection emerged as equally prominent themes.

Simone Biles, perhaps the most hyped Olympian before the Games, removed herself from early competition after developing the twisties — a gymnast’s version of the yips — before returning to claim a bronze medal. Naomi Osaka of Japan, who had lit the cauldron at the opening ceremony, exited in straight sets in the third round of the women’s tennis tournament. Novak Djokovic of Serbia, the top men’s player, lost his bronze medal match.

Even Caeleb Dressel, the swimmer who won five gold medals, lamented the strain of training an extra year — an unnatural cycle his coach had referred to as a “five-year quadrennial” — and the stress of making it through these Olympics.

“Some parts were extremely enjoyable,” Dressel said of his two weeks in Tokyo. “I would say the majority of them were not.”

Still, smaller, quieter moments glimmered through.

The camaraderie and celebrations of Gianmarco Tamberi of Italy and Mutaz Essa Barshim of Qatar, who decided, when offered, to share a gold medal in the high jump, charmed international viewers. So, too, did stories like that of Hidilyn Diaz, a weight lifter who claimed the first-ever gold medal for the Philippines, and Tamyra Mensah-Stock, whose sobbing interview after becoming the second U.S. woman to win gold in wrestling had a moment on social media.

Laurel Hubbard, a weight lifter from New Zealand, became the first transgender woman to compete at the Olympics, while nonbinary athletes whose identity does not fit neatly into longstanding gender categorizations also participated. One, the Canadian soccer player Quinn, won a gold medal.

Something resembling the Olympic spirit was, unexpectedly, often most easily observed in the newest sports, some of which were maligned as overly kooky when they were announced. At the sport climbing wall, competitors huddled to examine and discuss the configuration of holds on the walls, trading notes on how best to attack the challenges. At the skateboard park, rivals hugged and consoled Misugu Okamoto, 15, of Japan, who had cried after falling in the finals, lifting her onto their shoulders until she laughed.

Asked about the moment by reporters, she cried again.

“I’m grateful,” Okamoto said.

Not too far away, the Olympic Fan Park, a sprawling festival ground for ticket holders, sat dormant behind a padlocked fence, a sea of unused tables and attractions.

But Tokyoites found little keyhole glances of the Games, anyway. They glimpsed them on a train platform overlooking the BMX course, atop an overpass with a view of the sport climbing wall, from the side of the road as the cycling race whooshed by.

Modest crowds also gathered every night on a footbridge near Tokyo Bay, stopping and posing and taking pictures in front of the Olympic torch, even as security guards and volunteers halfheartedly asked them to keep moving. These were forgivable delinquencies, it seemed, for fans denied any other access to the Games. The mood was subdued but light.

“For some people who are paying attention, even enjoying watching it on television, it’s been gripping, I guess,” Koichi Nakano, a professor of political science at Sophia University in Japan, said of the Tokyo Olympics. “On the other hand, a large number of Japanese people are still terrified of the number of infections, which are going up, and the government’s inability to take action, at least in part because of the Olympics.”

Political controversies simmered — these were the Olympics, after all — but never quite detonated. Perhaps it was the I.O.C.’s deliberate pace on adjudicating any number of episodes — a Belorussian sprinter seeking political asylum; a podium demonstration from the American shot-putter Raven Saunders; two Chinese cyclists who wore pins depicting the silhouette of Mao Zedong — that kept each one from overtaking the narrative around the grounds.

Over the three weeks, questions about China, which will host the Winter Games early next year, when the pandemic is almost certain to still be raging, loomed large: To what extent would the I.O.C. and the athletes engage with issues of human rights in the country, like the mass detention of Uyghurs and other ethnic minorities? Did the restrictions on personal freedoms in Tokyo, enforced in the name of public health, augur more stringent rules in Beijing? Bach refused to take any questions about China at his final news conference on Friday.

The thing that will stand out from these Games, then, will be their strangeness, the way the established Olympic norms became juxtaposed with cutting reminders of these extraordinary times.

Wallechinsky, the historian, attended his first Games in 1960, in Rome. On Friday night he was debating whether to attend the closing ceremony, as he normally does. It would be a shadow of a normal ceremony, with many athletes, in the interest of public safety, already home. What would be the point?

He said he would rather remember the national stadium the way he observed it during one of the track and field competitions last week, when a small group of competitors had gathered in the prismatically colored stands, close enough to cheer for their teammates and friends. The scene touched Wallechinsky, he said. He could let the harsh reality of these Games wash away, if only for a moment.

“It felt a little bit like the Olympics,” he said.