Puppetron is a floating humanoid droid with a smaller clone resembling a marrionette. Puppetron has four yellow eyes and is wears a helmet.
- Attack: High
- Life: Tank
- Speed: Intermediate
Alter Ego 
Clones' Attack 
- ↑ Puppetron holds its clone, which then mimics a voodoo doll. The clone is slashed by red cuts while the same thing happens to the enemy.
- ↑ Puppetron summons four more clones and sends them all to "kamikaze" into the enemy, causing an explosion.
“You cannot say if he is alone or if they are two. A puppeteer maybe? Impossible to say, he makes us completely mad!"
- He is both a nod to Laughing Octopus and Screaming Mantis, from the Beauty and the Beast Units featured in Metal Gear Solid 4: Guns of the Patriots.
- Just like Psycho Mantis and Screaming Mantis, Puppetron appears to be a psychic.
- Instead of the regular 20% damage reduction to enemy attacks upon hitting with the curse ability, Puppetron has an 18% damage reduction instead. To compliment this, he has a slight increase in his HP pool.
- Even if it was a robotic mutant, strangely it doesn't have any Cyber gene.