WARNING: The following contains spoilers for Dr. Stone Chapter 229, by Boichi, Riichiro Inagaki, Caleb Cook and Steve Dutro.
After arriving on the lunar surface without much fanfare in previous chapters, Senku and his two crewmates came face-to-face with Why-Man, who is not a person but a collection of Meduas sharing a hive-minded AI that communicates via radio waves. Now, in Chapter 229, the AI known as Why-Man explains its plan in full.
The AI running the Medusas has had a symbiotic relationship with the human race, granting extended life inside the stone in return for being "fed" diamond batteries. Why-Man thinks this is a fair deal, but Senku objects, and he could easily compare this to the Machine overlords in the Matrix movies, keeping humanity enslaved in the virtual world of the Matrix. It's time to break free.
The Deal Why-Man Forced Upon Humanity
In Chapter 228, the Why-Man AI began its explanation of its plans to Senku's lunar team, and now in Chapter 229, Why-Man elaborates in greater detail. The Why-Man AI, according to its story, detected humanity as a sufficiently advanced race to tend to Why-Man's needs -- that is, feed it diamond batteries and protect it from harm.
Why-Man admits to being a parasite of sorts, forcing a symbiotic relationship upon humanity. In exchange for protection and nourishment, Why-Man offers eternal life to humanity via the petrification beams, and that stone can even heal people, hence Senku's "Dr. Stone" nickname for it. Why-Man prioritizes survival and eternal life above all else, so it falsely presumed that humanity would want the same and that humanity would be grateful for eternal life inside the stone.
Why-Man petrified the entire human race in the early 21st century, and for 3,000 years, Why-Man was left alone, unaware of how much harm the rays would do, proving just how little an AI would actually understand the needs of humanity. Why-Man meant well, but clearly, this AI is too reckless for its own good and used a heavy hand to promote this deal. Millennia later, Senku emerged from the stone and began reinventing humanity, eventually producing radio waves with his inventions.
Why-Man explains that once it sensed those waves, it failed to understand why humanity rejected its offer to build more Medusas or seek eternal life inside the stone, leading Why-Man to cry out "Why?" on the radio waves, inspiring its nickname. All this makes Why-Man a more benevolent version of the Machine overlords in the Matrix trilogy, keeping humanity "petrified" inside the Matrix world while using humans as living batteries -- a parasitic relationship between man and Machine.
Why Senku & Neo Reject The Machines
On one level, being healed by the petrification waves and living a comfortable and ordinary life inside the Matrix seems appealing. The Medusas can heal the human body better than any Stone Age medicine, and life inside the Matrix is much more comfortable than the hardscrabble life inside the Nebuchadnezzar or Zion, living in constant fear of the machines deep underground. That's why Cypher betrayed Morpheus' crew to Agent Smith; to trade his miserable life in the real world in exchange for blissful ignorance in the Matrix. Meanwhile, in Dr. Stone, Why-Man evidently expects humanity to feel the same way, but instead of meeting a Cypher on the moon, Why-Man meets Neo -- Senku himself.
Senku and Neo both face tyrannical machines who treat humanity like crops to be cultivated, and these stories continue a vital theme in science fiction -- that while machines and technology can be useful, they must not control the future. Humanity must decide its own future and succeed or fail on its own merits, and as a shonen series, Dr. Stone suggests that the power of hope and friendship will always be stronger than the deal with the devil that Why-Man offers. Eternal life is overrated -- Senku would rather rebuild humanity with his friends, and now, he must convince Why-Man to see things his way. The final clash has begun.
