I suspect during the events on God Valley (38 years ago), Rocks betrayed his crew in an attempt to escape when he realised they couldn’t defeat Roger and Garp and as a result of that betrayal, Kaido (whom respected Rocks and was left in a state of shock) was captured by the Marines and taken to the World Government research facility on Punk Hazard. Since that moment, Kaido’s perception of pirates and the world became warped.
Personally, I do not believe Kaido had Ancient Giant DNA injected into him while being experimented on but rather I believe Kaido was linked to the Ancient Giants from birth through his blood. It would not have been possible to manipulate an individuals DNA before Judge and Vegapunk discovered the Lineage Factor around 25 years ago. Vegapunk only "joined" the Marines as a Scientist after that discovery. If the World Government/Marine scientist(s) were the ones who turned Kaido into what he is by instilling Ancient Giant DNA into him, they would have been ones who discovered the Lineage Factor first - Kaido’s younger self silhouette from his Rocks Pirates days 39+ years ago showed him with Ancient Giant-type horns. As that did not happen, I highly doubt Kaido's DNA was modified to transform him into a part Ancient Giant. Kaido may be a very unique variant of the Ancient Giant or only part Ancient Giant (his base form isn't as large but when he transforms into a Dragon, possibly his Ancient Giant genes kick in to enlarge the Dragon form).
Once Kaido was captured and imprisoned, it was likely Big Mom who help free Kaido from Punk Hazard. Big Mom had mentioned to Kaido before leaving for Wano Kuni of a debt Kaido owes her from the past. Could the debt she is referring to be the time she saved him from the World Government Science research facility stationed on Punk Hazard? That certainly would count as something Kaido would owe Big Mom big time for. If this is the case, this could explain why Big Mom knows about the Punk Hazard research such as the gigantification experiments. They were part of the same crew prior to the God Valley incident, so before their relationship eroded into what it is today, Big Mom may have felt desire to help Kaido as a result of the kinship they once shared.
Big Mom’s time on Punk Hazard may have also been where she attained a copy of the Punk Hazard lab blueprints.
After Kaido escaped, the World Government scientist could have used the existing research and DNA samples of Kaido (if he is part Ancient Giant) or any future samples they procured from Kaido on subsequent captures to conduct their research on the Ancient Giant creation project - at least over 20 years ago considering Jaki is present during Oden's flashback. Kaido’s DNA and any other Ancient Giant samples the Punk Hazard scientist had may have been used as the foundation for experimenting on the prisoners they had as test subjects (failed Numbers experiments). It would explain why the "Numbers" ended up developing certain features and tendencies similar to Kaido, mainly the horns and the love for alcohol. Kaido and the Numbers also share in the use of the same type of weapon – kanabō. Kaido could have realised the connection he had with the "Numbers" when they went up for sale on the black market and consequently purchased them as Big Mom mentioned.
Lets take that one step further. In addition to the Numbers, I can see Dragon Number Thirteen and the smaller dragon being based on Kaido’s DNA assuming he had his Mythical Dragon Zoan Devil Fruit while a member of the Rocks Pirates. The naming convention of the Numbers and Dragon Number Thirteen suggest some connection regardless of the Dragon being named by a Tenryuubito. Once Vegapunk joined the World Government, which would have been after Kaido escaped, he could have used the research and samples on Kaido to conduct his experiments on gigantification (Ancient Giants) and on his own research involving dragons.
Ultimately though, Vegapunk was unsuccessful in his gigantification experiments (Numbers?) though he did succeed in producing dragons via Dragon Number Thirteen and the smaller version Dragon. Vegapunk has already shown his capability in isolating Devil Fruit powers by utilising the Pika Pika no Mi to develop the explosive lasers for the Pacifista. He may have first attained that knowledge through the experiments done utilising Kaido’s DNA samples and research. The reason the Dragons survived the Shinokuni poison from four years ago when Caesar activated his weapon and the battle between Sakazuki and Kuzan could be the result of having Kaido’s DNA. The DNA would have also allowed those experiments to breathe fire and attain their thick skin.
And even beyond that, there is the possibility that Queen and King were also prisoners on Punk Hazard being experimented on. With Queen, that scar running down his right shoulder and chest could be the result of experiments, particularly because of its stitched nature. Queen may have also developed an interest in weapons and viruses because of his exposure to the World Government science labs. King is an interesting case due to the rare race he belongs to but I wonder if the experiments done on him caused his wings to turn black and to produce the plume of fire rising from his back. Taking King's appearance into account, it seems possible that he may have been experimented on. The experiments on King could have caused an issue with his skin which is why he now covers his whole body and wears a full-faced mask. King’s suit could be something he acquired from Punk Hazard. Additionally, if Vegapunk had access to King’s DNA samples, he may have used it in conjunction with Kaido’s DNA to help add wings to the Dragons he created. As a result of Kaido freeing the two of them, they may have swore their allegiance to him and been the start of the Beast Pirates. This could be one way to tie Kaido, King and Queen's backstory together to quicken the pace of the Wano Kuni Arc story.
Turning to Vegapunk's Artificial Devil Fruit, he likely based it off Kaido's Mythical Dragon Zoan Devil Fruit. The resemblance in Kaido’s and Momonosuke's Dragon transformation seems too homologous to be coincidental. I believe Kaido’s DNA (including his Dragon aspect) was used as the base to create a Dragon which in turn was used to create the Artificial Devil Fruit. Vegapunk would have likely used his (and Judge’s) findings on the Lineage Factor to isolate the Dragon aspect of Kaido’s Devil Fruit via the DNA sample to base his research on the Dragons and eventually the Artificial Devil Fruit project.
With Punk Hazard holding much relevance to the science experiments conducted within the One Piece world including the Numbers, SMILEs and possibly Seastone Chains which are connected to the Beast Pirates, it seems appropriate for Kaido to also have a direct connection with Punk Hazard. Knowledge of the research done by the World Government scientist could have been acquired by Kaido through his time as a prisoner and research subject there. Additionally, Big Mom’s knowledge of Punk Hazard and her relation to Kaido also suggest a connection there which could be linked to the debt Kaido owes her. Kaido being a prisoner on Punk Hazard does appear to tie those elements together.
Thank you for reading.
