When Senku was a first grader he decided that he wanted to go up into space. In the middle of class he made a statement about how he was going to go up into space. When his teacher told him that becoming an astronaut was a wonderful dream, to which he responded that he was going to do it right away. It was ever since that moment that he fell in love with science and started fighting for his dream. he knew practically nothing about science at the time but he read many books and tried out many different experiments, learning more and more over time with the help of his father. Sometime after he began his experiments, he had Taiju, his best friend, help him run errands for whatever was needed in the experiment. Whether they were friends before this is unknown. Several years later, Senku said that he wanted to try having some light objects in the rocket that he made. Taiju wanted to help and so he asked Yuzuriha to make knitted stuffed toys of herself, Senku and himself. Taiju asked her this because she was a member of the handicrafts club. Senku put the three stuffed toys inside of the tiny rocket that he made and sent it up into the air. The rocket did not make it all the ways to outer space but it shot the stuffed toys out to space. Ever since then Senku, Taiju and Yuzuriha have been very close friends.
Senku first appeared in Chapter 1 of Dr. Stone as a high school student wearing a lab coat. When Taiju declared that he's going to confess to Yuzuriha, Senku offered Taiju a "potion" he proclaim will give Taiju a Ten Billion Percent Chance of success. Taiju refused it saying he wanted to confess and receive a genuine answer from Yuzuriha. Senku then revealed the other classmate that the potion was actually made of gasoline and would kill Taiju had he drank it. But he was Ten Billion Percent sure that Taiju would refused it. Afterwards, the petrification came and Senku was frozen in place.
While petrified, Senku, who is still conscious, begin to count the time of his petrification. Upon depetrifying, Senku has counted up to 116,427,065,520 seconds meaning that he's been petrified for 3,689 years and 158 days. Free from his petrification, Senku begin to plan and build towards sustaining himself. That's when he came upon a petrified Taiju and decided to find way to depetrify people. He trace back to the spot where he was depetrified and discover that Nitric Acid was the cause of his depetrification. Thus, he begin to test his theory out by applying Nitric Acid to petrified birds and humans but to no avail. He surmise that adding alcohol, which comprise of Ethanol will turn Nitric Acid into Nital, might help with the depetrification. However, he didn't have any alcohol and doesn't have a means to obtain it thus came to a dead end. That's when Taiju depetrified on his own and met up with Senku.
With Senku as the brain and Taiju as the brawn, they begin to worked together in order to survive and find a way to depetrify other people. That is when Taiju come upon some wild grapes in the forest and suggest the idea of creating alcohol through the wild grapes. After creating alcohol using the wild grapes, Senku is ready to test out his theory on Nitric Acid and Ethanol. To their surprise, Nital is the formula that can depetrify people. Thus, they finally came up with the formula of depetrification. And being the one who found the wild grape, Taiju decided that the first person they should depetrify is Yuzuriha.
As they attempt to depetrify Yuzuriha, they were attacked by lions and is forced to free the petrified Tsukasa, the strongest primate of high-schooler. Upon being freed, Tsukasa displayed his unbelievable level of adaptation and strength when he quickly understood the situation and proceeded to kill the leader of the lions with a single punch. Freed from danger and having ran out of Nital, they all return to their hideout with a petrified Yuzuriha.
While at their hideout, Senku begin to talk about his plans of revive humanity to the modern age through the four uses of Calcium Carbonate in sea shells. But as Tsukasa begin to show displeasure about Senku's plan of reviving modern humanity, Senku decided to only revealed three of its use which was agriculture, architecture, and medicine. on their way to procure sea shells, Senku gradually begin to notice Tsukasa desire to maintain the status quo as he destroy petrified statues of old people and suspect that Tsukasa will betray them.
For precaution, Senku send Tsukasa to procure more Nitric Acid as a faint to buy them time on what to do. With Tsukasa exiting, Senku quickly told Taiju to free Yuzuriha with the Nital he procure and explain to Taiju that they only have two choice. They either stand and fight Tsukasa or run. But before they can decide, they were stop by Tsukasa who intend to preserve a primitive world. Tsukasa believe that it would be better for humanity if the world to remain primitive where nobody owns anything and everything is free for grabs. With his intentions clear, Tsukasa begin to attack Senku and the others in attempt to force them to surrender. But with no idea what the formula for depetrification is, Tsukasa decide to retreat in order to give time for Senku and Taiji to surrender.
With the time given to them, Senku told them to escaped while making it seem like they ran between their tails. In truth, Senku already has a plan of defeating Tsukasa as he revealed the fourth use of Calcium Carbonate which is for warfare. In other words, gunpowder. They quickly made their way to Hakone to procure Sulfur and added to the Charcoal and Saltpeter that they have in order to create black powder. As they begin to test their powder, Tsukasa, who was not fooled by their faint, realize what they're doing and is coming after them.
At the summit where they tested the gun powder, Senku, Taiju and Yuzuriha noticed a smoke signal confirming the presence of other humans other than them. They wanted to send a signal fire back but that will give away their position to Tsukasa, Finally after some deliberation, Senku told Taiju to light up a smoke signals themselves to establish contact with the unknown human.
Upon seeing the signal, Tsukasa caught up with Senku and took Yuzuriha as hostage. He bargained with Senku for the depetrification formula on exchange for Yuzuriha. Senku agreed and gave him the formula. Tsukasa then once more ask Senku to stop trying to advance humanity and join him for he did not want to kill Senku. Senku happily decline saying that that's the only thing he cannot do. Tsukasa proclaim that had they met 3700 years ago, Senku might have been his first friend. With a heavy heart, Tsukasa broke Senku's cervical plexus which resulted in Senku dying.
As Taiju return from lighting the smoke signals, he witness an unconscious Senku on the floor with Yuzuriha in tears. Realizing what has happened, Taiju charge towards Tsukasa as he threw a boulder into the air. This distraction helped Yuzuriha to throw gunpowder on Tsukasa which exploded when the boulder hit the ground and allowed Yuzuriha and Taiju to escape with Senku. Tsukasa decided not to go after them knowing full well that Senku could not make a recovery in the stone world.
As Yuzuriha and Taiju stop to examine Senku, they notice that part of Senku's neck is still petrified which might have protected him from Tsukasa's blow. They quickly applied the depetrified formula to Senku neck hoping that he'll awake. After crying out to Senku many times, Senku manage to came back to his senses. From there, Senku asked Yuzuriha and Taiju to return to Tsukasa's empire as spies so that Senku can keep taps on him. Thus, they part ways as Senki venture out by himself to build his Kingdom of Science to combat Tsukasa.
On his travel, Senku meet Kohaku, the person who lit up the smoke signals. She was defeated by Tsukasa and was underneath a tree which rendered her unable to move. Senku helped her lift the tree with the use of pulleys which she thanked him for. She even went as far as proclaiming her love for Senku and applaud him of his gallantry for sacrificing his life to save Yuzuriha which she bear witness to. She then ask Senku to go with her to her village because she was astounded by his science which she refer to as "sorcery". After talking to Kohaku, Senku realize that Kohaku and her village are descendants of humans who were able to avoid the petrification 3700 years ago and survived since then. Meaning that they grew up not knowing the modern world.
Upon arriving at the village, Senku was attacked by Kinro and Ginro who suspect him of being an exile. After astounding them with his soap bubbles "sorcery," Senku was confronted by Chrome, the self proclaim "sorcerer" of the village. Chrome challenge Senku to a sorcery battle with the stake being all his life gathering and himself versus Senku kneeling before him and promising to never step foot near the village again. Chrome, of course, was utterly defeated by Senku and had to surrender everything to Senku.
After examining the things that Chrome had, Senku decided to make Kinro a golden spear by dipping the edge of his spear with melted mercury mix with gold dust. Though it had little effect in winning Kinro over, Ginro, who wanted a silver spear to match his name was convinced. Senku then explain to Chrome that everything Chrome has done is not sorcery but science. And that Chrome is the first scientist to ever been born in the past 3700 years. Testament towards Tsukasa that no matter how much Tsukasa try to hinder humanity's advancement, there will always be someone out there to challenge it and push it forward.
Soon after settling down, Kohaku revealed to Senku that her sister, Ruri, was sick. And that Chrome has being trying to find a cure for her. Wanting to get the village to trust him more, Senku proclaim that he has a cure-all medicine that might work on Ruri. The cure he's talking about is Antibiotics. He explain to them that they can either go towards the Sulfur drug route or the Penicillin blue mold route to make antibiotics. They decided to take the Sulfur route due to it being more abundant in this era.
As they try to gather the ingredients to make Antibiotics, Chrome point out that the earth was spinning. To Senku surprise, he notice that the north star has shifted due to earth tilting after 3700 years. Which lead Chrome to showing Senku him his magnetic rocks that acted as compasses to point towards north. Realizing that they posses magnet, Senku ask them to use the magnet to gather Iron from the river. Thus the Iron age has dawn once more on Earth..
While gathering more Iron at the river, they met Suika, who was helping them secretly. She proclaim herself to be useless but Senku deter her from thinking that way. Senku told Suika that her help is much appreciated and that everyone is welcome under his Kingdom of Science. Seeing Suika get swept away by Senku's words, Chrome reference that Suika is Momotaro, a fictional children story of modern time. When ask why Chrome would know something that existed 3700 years ago, Chrome and Kohaku explain to Senku that it's a story told by Ruri who is the priestess of the village. Senku then realize that despite 3700 years, there are stories that are past on to the next generations which peak his interest in Ruri. Upon hearing that Senku is interested in Ruri, Chrome blurt out his displeasure revealing that he is in love with Ruri.
After gathering enough Iron, the crew return to the village outskirt so that Senku can prepare a furnace to melt the iron. In order to melt iron, they need to reach a temperature of 1500 Degree Celsius which isn't enough for burning wood can only produce up to 700 Degree Celsius. Thus, they resort to adding more air to the fire in order to increase the temperature. But due to the lack of man power, they were unsuccessful in melting the iron. Needing more manpower, Senku ask Suika to infiltrate the village and find out what the village want in order to bribe them into helping.
After finding out that better tasting food can buy the help of the village, Senku ask the team to gather Green Dogtail to grind to flower and then make Ramen. The plan was a success which drew out many villagers to help Senku for Ramen. But during their cooking section, they were intrude by Asagiri Gen, a modern day Magician who is currently working for Tsukasa. Tsukasa send Asagiri to make sure that Senku is truly dead, but with Senku now being able to produce iron, Asagiri is having second thoughts on supporting Tsukasa. He then ask Senku to give him a reason why he should support Senku's cause. Senku told him that with the power of science, he will bring back electricity and the applications that goes alone with it. And with the metal the melt with the effort of the village, Senku was able to build a mechanical electricity generator.
Just before Asagiri can make his decision, he was stab by Magma who mistook Asagiri for Senku. While being cure back to health by Senku and the others, Asagiri ask Senku if he's able to make a bottle of cola cause he's dying to drink one. Senku told Asagiri that he is 10 billion percent sure he can make one. And with that promise, Asagiri return to Tsukasa and lied to him that Senku is truly dead.
Having thought that he killed Senku, Magma proclaim himself the most powerful out of the village who will marry Ruri and take over the village as Chief. This is when Chrome and Kohaku explain to Senku that the village is holding a tournament in a few months in order to decide the next chief. Since Ruri, the priestess of the village, has turn 18, she will have to marry the winner and become the new Chief's bride. They than explain that Magma only has eyes on the Chief seat and feels nothing for Ruri. Rather, he would prefer Ruri to die once he become Chief so he can do what he want. Seeing this as an obstacle to his plan of saving Ruri and gaining the village's trust, Senku entrust Kohaku with the task of defeating Magma while he and Chrome continue their mission on creating antibiotics. Kohaku confronted Chrome saying that he should have been the one to marry Ruri since he loves her most. But since Chrome was weak in combat, Kohaku has to resort to training Ginro and Kinro instead. Chrome reply that it doesn't matter to him as long as he can save Ruri's life and make her happy. And thus Chrome and Senku continue to work hard on making antibiotics.
In order to formulate antibiotics, Senku requires beakers and flasks which can withstand acid. Thus, Senku decided that the next thing they should gather is sand which contains silica used to make glass. With everyone's help, they were able to gather enough sand and produce their first glasses. Glasses that Senku use to produce lenses in order to help Suika, who is nearsighted, see. Afterwards, it was quickly discover that Kinro too was nearsighted and is the root cause to why his fighting ability was so poor despite his talent. Yet, even after discovering that he can cure his sight with glasses, Kinro was too proud to ask Senku for help.
Although they now have the ability to make glass, without proper technique and experience, Senku and the other weren't able to create what they needed. Thus, they resorted into kidnapping Kaseki, the craftsman of the village. At first, Kaseki refuse to help. But after being peaked by the fact that Senku can produce glass and was angered at how wasteful and terrible Senku and the others is at making it, Kaseki reluctantly decided to help them. And with Kaseki's help, they were able to create the perfect lab for Senku to use. And seeing the lab, Senku can't help but reminiscent about the time his father sold his car to buy him a lab.
While in his lab, Senku was intruded by Ginro and Kinro with Ginro proclaiming that since Senku has so much, surely he can make a silver spear for the two of them. Senku smile, Senku offer to make Ginro a silver spear but only if Ginro is willing to help them find the hardest formula for antibiotics. Ginro agreed and thus Senku made him a silver spear. But little did Ginro know that the silver spear Senku made for him is going to be used to detect a poison so deadly that it can kill a person within seconds.
As them make their way to the top of the mountains, Senku warned Ginro that he best focus the point of his spear far ahead of him because once the silver on his spear turns black, that will signal his death. Senku then explain that the item they're going to procure is call Sulfuric Acid which only exist at the top of the mountain inside an emerald lake. But the emerald lack produces the poisonous gas call Hydrogen Sulfide and Sulfur Dioxide that is as deadly as it sounds. In order to detect the distant of the gas, Ginro spear will be use because Hydrogen Sulfide and Sulfur Dioxide will react with silver, turning it black.
After gauging the distant of the poison gas, Senku and the others return to their home in order to produce protective masks that can filter the poison. But upon making the mask, Senku told Chrome to stay while Senku alone will go to procure the Sulfuric Acid. Chrome contest saying he too would go with Senku Senku then remind Chrome that they are the only two scientists left in existence and one of them has to survive. Senku volunteer himself to go because he has a higher change of getting the Sulfuric Acid unharmed due to his knowledge. Senku is ready to pass on his knowledge of science to Crhome before he live when Chrome out right refuse it. He told Senku that two scientists on the job is better than one and that failure will not be an option, thus convincing Senku to let Chrome go with him.
When they reach the Emerald Lake, Senku advice Chrome to not be overcome with fear for heavy breathing can cause the mask filter to not work properly and can lead to his death. They approach closer to the emerald lake but as acid spew out and burnt part of Senku's mast tube. Chrome was able to warn Senku in time but lost his step and start to fall into the emerald lake. Luckily, Ginro arrive in time with his own mask to save Chrome from falling. They were able to procure the Sulfuric Acid and return home to make the antibiotic.
Now the only thing they need to make the antibiotics is alcohol to which Kaseki reminded then that they can get from the village if they win the tournament. Back in the village, Kohaku is training Kinro heavily in order to beat Magma in the tournament. With Senku's return, he, Chrome, and Ginro along with Kohaku decided to enter the tournament to procure the alcohol and to increase their odds of winning. Their goal is to weaken Magma before his fight with Kinro which will give Kinro a bigger chance of winning. However, it was determine by coincidence that Kinro and Magma will be fighting on the first match. With their plan ruin, the team can't help but pray that Kinro wins the fight.
As Kinro engage Magma, he was able to fight evenly in close combat. But as Magma increase the distant between them, Kinro battle ability begin to deteriorate due to his poor eyesight. That is when Suika threw her helmet which contain the glasses that Senku made for her at Kinro. Now being able to see with the help of Suika's glasses, Kinro overwhelmed Magma and stood victorious. But as Kinro talk to the judge about getting assistant from Suika has unfair, Magma struck him from behind and became the victor of the first round.
The second round is between Chrome and Magma's lackey. After getting warned that Suika was seen being washed away by the riverside, Kohaku abandon her place in the tournament so she can go to save Suika. But little did she know that Suika was safe and has returned. Which means that Chrome must prolong his fight in order to give Kohaku enough time to return. Just when Kohaku was able to come back, Magma order his lackey to surrendering which disqualified Kohaku from the tournament and Senku win by default.
The next fight is then between Ginro and Argo. As Ginro realize that he might not win the match, he once more begin to gorge the herb Senku gather claiming to help with stamina. And believing that he was empowered by the herb, Ginro was able to win the fight with his imaginary strength. But due to his recklessness, he suffered a huge amount of injuring and fainted.
The next match is then between Chrome and Magma. With Chrome being obviously weak in fighting, he was pummel by Magma. But with his will to never give up, he stood back up with Suika's glasses hanging onto his spear. He was determine to concentrate the energy of the sun with the glasses in order to burn Magma. But in order to do it, he needs to gather enough water on the glasses so that the concave index of the glass become convex. Then he has to make sure that Magma remains still for a minute in order for his clothe to burn. Luckily, Asagiri arrive at the right time. Surprise that Asagiri is still alive, Magma was trick into standing still by Asagiri long enough for Chrome to light his crotch on fire. To put out the fire, Chrome landed a devastating blow onto Magma's crotch and knocked the wind out of him. The battle was won and Chrome was the victor.
The next match is between Senku and Ginro. It was obvious hat Senku's plan worked. With Magma out of the picture, all they need to do now is throw the match for Chrome to win. But with Ruri proclaiming that she will dedicate her life to whoever wins, Ginro betrayed Senku and started to fight in order to win and become Chief. Annoyed with his intentions and betrayal, Senku uses Suika helmet that was laying around as a leverage to knock the wind out of Ginro's crotch. Senku became the victor in the match.
With only Senku and Chrome as the contestant, Senku was determined to surrender so that Chrome can at last be with Ruri. But to Senku's surprise, Chrome fell unconscious during the match and Senku was made the winner. Senku who reluctantly refuse to marry Ruri was happy to accept the alcohol that was given to the winner. When the chief told Senku that he is married to Ruri by right, Senku merely state that he wanted a divource and escape to his lab to create the antibiotic.
Now with all the recipe, Senku is on the process of going over the 25 steps in making antibiotics. Asagiri, who is just wasting around, was confronted by Kaseki and was forced to help out. After everyone's effort, Senku was able to make the antibiotic and thanked everyone for the help. As for Asagiri, Senku was able to make a cola and left it for him as they promise.
Senku quickly enter the village and gave the antibiotics to Ruri. But instead of improving her situation, the antibiotic worsen her health which the village chief scorn Senku for. But for Senku, it was a good thing because the symptom that Ruri is now showing has pave the road to determine the sickness. Senku determined that Ruri has Pneumonia. Senku suggest attacking the illness by using sulfa drugs but Ruri's father rage in contest, forbidding Senku in feeding his daughter anything. That's when Chrome, Kohaku, Kaseki, Ginro, and Kinro voice their opinion and their support of Senku's action. Having so many people with their faith on Senku, Ruri's father concede and Senku was able to cure Ruri.
With Ruri cured, the village finally allow Senku into their ranks and proclaim him as their chief. To Senku's surprised, he finally learn that the village was named Ishigami which is Senku's last name. Ruri then approach Senku stating that she has heard story from her mother, the previous priestess, about Senku and his father Byakuya. This made Senku realize that everyone in Ishigami is a distant relative of his. They were descendants of his father who avoided the petrification because he went on a mission to outer space. This brought back Senku's memories of his father and how he helped his father became an astronaut. And the person who created the village that they were in is his father Byakuya Ishigami.