One of the smartest recent anime, with one of the catchiest opening theme songs, Dr. Stone has many intelligent characters that create incredible inventions that make life easier for those around them. Senku and the Ishigami villagers collaborate on projects that would be insanely difficult even in modern times, let alone in a stone-age world.
While the anime is not about time travel, Dr. Stone explores what it would be like if the world's progress was forced back thousands of years. The most intelligent characters navigate the Stone World, forging their knowledge by learning more about the world around them.
Homura Momiji
Homura's speed and dexterity make her an excellent assassin and tracker. Her intelligence allows her to be Hyoga's right hand, surveying Ishigami Village on behalf of Tsukasa's army and working closely with Hyoga to accomplish his goals. She possesses a great memory, able to remember the faces and names of every villager despite only knowing them very briefly.
She is difficult to track and rarely gets tricked or flustered, maintaining composure even in difficult circumstances. She was the first to notice the sulfuric acid gas when even Hyoga hadn't sensed it, and she even outwitted Senku when he marked her with tungsten to track her, washing off the marker to confuse the villagers.
Ukyo Saionji
Although Ukyo is a pacifist, he is an incredibly skilled combatant with his super-sensitive hearing and pinpoint accuracy when shooting his bow. In the previous world, Ukyo worked as a submarine sonar operator, a career that clearly requires accuracy and intellect.
Ukyo is also a great tactician, as he was able to take advantage of Chrome's smokescreen when attacking him, concealing his own position. Ukyo can speak both Japanese and English, and, later in the manga, Ukyo even becomes one of the Five Wise Generals, helping to run the Kingdom of Science.
Kaseki
A passionate and skilled artisan, Kaseki is instrumental in creating glassware and inventions for the Kingdom of Science. He is a genius at identifying materials and knowing exactly how to manipulate them. For example, he can see glass and immediately understand its properties and how it can be made and used.
Crafting techniques are his specialty, but Kaseki quickly picks up skills in other areas of science such as chemistry and mechanics. It is very fortunate for Senku to find such a skilled person in a primitive village, but later episodes of the anime imply that Kaseki's knowledge was passed down from the original settlers of Ishigami Village, which makes a nice personal connection between Senku and Kaseki.
Hyoga
Kyoya is an extremely dangerous character that is instrumental in the Stone Wars, one of the best wars depicted in recent anime, constantly causing havoc for both teams. He is clear-headed in combat, thinking on his feet and adapting his plans to whatever the enemy might throw at him. He is cautious and analyses the battlefield before proceeding, and he puts his faith in those he deems can "do the job properly," such as Homura.
Kyoya can also manipulate others well, like when he to be on Tsukasa's side before betraying him. In addition to being one of the most powerful soldiers in the Stone Wars, he is a tactical genius that earns quite a few victories on his own merits.
Gen Asagiri
Originally an enemy of the Kingdom of Science revived by Tsukasa to rival Senku's intelligence, Gen is an incredible tactician and psychologist. He utilizes trickery to his advantage, and he's able to predict what others will do as well as manipulate them into thinking or doing what he wants. Gen is an adept liar, impersonating Lillian and easily fooling those he wants to manipulate.
Gen carries a good knowledge of the human mind and is able to find out exactly what makes others tick, making them easier to control. He is also bilingual, speaking English and Japanese, and is a master of sleight-of-hand tricks, being a magician in the previous world.
Chrome
A curious and inquisitive character, Chrome was born into the Stone World and so had to earn all of his scientific knowledge from scratch. He is seen as weird in Ishigami Village for exploring science, as the inhabitants call him a sorcerer and distrust him, but this noble pursuit aids Senku immensely and makes Chrome one of the smartest Stone World inhabitants.
Chrome has deep knowledge of chemicals and materials that can be found in the Stone World, having investigated them all his life. Chrome is brave, loyal, and very quick on his feet, jumping to defend his friends and use his scientific knowledge for good. He's of above-average intelligence when it comes to math and calculations, but this is quickly surpassed when Senku and the other modern humans are unpetrified.
The Space Crew (Shamil, Darya, Yakov, And Connie)
Connie Lee, Shamil Volkov, Darya Nikitina, and Yakov Nikitin were the inhabitants of the International Space Station before the petrification event. Lillian was also part of the space crew, but she was not a scientist, having reserved a civilian seat on the space station.
Darya and Yakov worked together in a lab aboard the space station, and Yakov is the only astronaut to be on the space station for a second time, proving that he is a capable astronaut that is trusted by the station's overseers. Astronauts usually go through years of intense training before setting foot in space, so the space crew undoubtedly surpasses even the most intelligent of the revived humans in the series, with the exception of a few gifted individuals.
Byakuya Ishigami
Byakuya was Senku's adopted father, a playful and kind-hearted man that worked extremely hard to give Senku a good life. Senku inspired him to go for his dream and become an astronaut, forcing Byakuya to work hard and study to be chosen as one of the few to live on the International Space Station. Byakuya is extremely intelligent, passing the tests and becoming an astronaut, as well as leading the astronauts to create a new village after the petrification event.
Senku's realization that Byakuya is no longer around is a heartbreaking moment in the anime, as Byakuya was a major source of inspiration for him, nurturing his scientific talent and teaching him to reach for the stars. Byakuya also demonstrates his intelligence by leaving behind a coded message in the Hundred Tales for Senku and recording a CD for him to play once Byakuya is gone.
Tsukasa Shishio
Tsukasa wants to make a strong world of warriors, calling his camp the Empire of Might. Initially, he tries to coexist with nature and only revive strong people to prevent the world from making the same mistakes as before, creating pollution and causing harm to the environment. His goal becomes less than honorable, however, as he goes around smashing petrified statues to cull innocent people whom he believes to have been weak.
His intelligence is boundless, often accurately predicting Senku's plans and strategies. He possesses some knowledge of biology, accurately targeting Senku's neck when attempting to kill him, and has knowledge of chemistry, as he realized along with Senku that the anti-petrification liquid was made of citric acid.
Senku Ishigami
The absolute genius of Senku cannot be understated, as he has created some insanely difficult crafts throughout the series. From the very beginning, Senku counted the seconds that he was petrified, therefore making him able to calculate the correct date in the future. He believes in science to a fault, but explains complex scientific methods clearly to the villagers, and, by extension, the audience.
Senku is selfless at heart, but his outward persona is arrogant and determined, ensuring that everyone around him has faith in his abilities by showing what great inventions he can make. His encyclopedic knowledge progresses humanity throughout the series and helps him to think on his feet, using his knowledge to save people.