Dr. Boshi created the clone scientist to be close to perfect clones of himself that would work with him. The clones were not perfect clones of Boshi, and had very little individual personality. They may talk with each other via their hand held pads.
Clone scientists, although attempted clones of Boshi himself, are completely made of metal and are 0% organic. Clone scientists contain large valuable brains inside their titanium bald heads, with Boshi's hair drug failing to work on their noggin. Not only is their head made of titanium, their entire body is made of it.
Their titanium bodies protects them from death, as Takeshi's ninja stars cannot penetrate them. Clone scientists can be stunned by being tossed to the ground, which will shut them off temporarily. The metal scientists perpetually carry around small pads which can be used to alert the security, control parts of the building, or for talking with other Clones.
Clone scientists possess abilities beyond most enemies, but are limited to walking short distances and lack attack. They will walk short distances while on a platform, walking a bit then gazing down at their small pad. They will soon turn around and walk the other way. Clone scientists are unable to leave the platform they are on, and act more like security guards than scientists, as they cannot attack or harm the player.
A clone scientist will set off the security when they spot Takeshi, the clone scientist facing the screen with orange eyes. Takeshi can pass them when they have their backs turned, but the slightest glance will cause them to set off the alarm. Takeshi can pass them by stealthing and waiting for them to pass, or by masquerading as them. By shooting a ninja star at a clone scientist, the clone will be presumably knocked out and slam hard on the floor with a metal clunk.
Their eyes will not be lit anymore, the player free to pass them while they are down. They will come back up in about five seconds, and will not set off the alarm even though something rather unusual has happened. The alarm will not go off if a clone is knocked out or glimpses a ninja star, even though these actions are rather unusual. Clone scientists are rarely seen in groups, them often found alone on one platforms, usually inside a box like structure with the two force fields on each end.
A unique part of Final Ninja Zero is how the player can play as a clone scientist. By obtaining a power orb, they have to next stun a clone scientist, jump down to the scientist's body, then press the arrow key. They will assume the form of a clone scientist, only with glowing green eyes instead of glowing orange eyes. They can only masquerade as one clone scientist per one power orb, the player only being able to carry one power orb at a time.
When they are a clone scientist, they can walk, jump, wall slide, or stay completely still, and no other clone scientist or enemy troops will notice Takeshi's unusual movements and green eyes. Takeshi runs, jumps, wall slide and wall jumps as fast as when he was in his ninja suit, and can walk past enemies without damage since he appears as a clone scientist. There are some actions Takeshi can perform in their ninja suit, but not in their clone disguise, such as shooting a ninja star, or pressing the down arrow key ( ).
Doing any of these actions (clicking anywhere on the game's screen will be interpreted by the game as shooting a ninja star) will cause the player's disguise to fade, revealing them to be Takeshi. Being harmed by a hazard, bullets, or explosive capsule will also reveal the player. Upon being disguised as a clone, the player will have only 20 seconds to get where they have to get to before their disguise wears off, this disguise completely necessary for traversal of clone scientist infested territory, if it coming off in this area the player will surely be killed.
Usually where the player's disguise will come off, a space will usually be nearby where the player can hide and obtain another power orb. Power orbs are found close to the laboratories of clones, where many clones are present that would make traversal of the area under normal circumstances hard or impossible.
- Factory - A clone scientist appears being assembled. The picture shows an image of a metal scientist moving toward the painting station.
- A message from one of the clones can be intercepted in Final Ninja Zero, about a clone telling another clone why he made faces behind Dr. Victor Boshi's back.
- Another message can also be found about a clone scientist wanting to explain a "joke" to the other clones, and its side effects.
- The Factory skin, where the clone scientist appeared was coincidentally released exactly one year after the release of Final Ninja Zero.
- Possibly due to deadlines or simplicity, Dr. Boshi's entire body; except his head, is the body of a clone scientist. The animations of Boshi running and jumping are the animations where the player runs and jumps as a clone scientist, only Boshi's animations have the head of the clone scientist replaced with Boshi's head. This is probably to show how Boshi and his clones are alike in appearance, or possibly because it was more easy to have Boshi's head on a clone scientists body than it was to make an entirely new body.
- In another level of Final Ninja Zero (titled 'cloning laboratory'), the background shows multiple clones in tanks. Furthermore, these clones are naked, but their entire torso is covered by metal.