In an alternate universe from the main R-Type games, the Space Corps and the Bydo Empire have ended a long ongoing conflict with each other and have finally made peace. As a result, humanity begins a large and ambitious technological project called Project Paradise, which concentrated on the creation of a new planet called Eden for human colonization, with a powerful bio-computer called Major being placed as head of the project. However, not long afterwards Major suffers a malefaction and turns hostile on humanity as a result, building an army of defenses to invade Earth and destroy humanity.
Since the R-9A Arrowhead is presumably retired in this universe, the Space Corps sends a newer R-Type model to counter the new threat called the R-9 Leo. This craft differs from other R-crafts as it lacks a Force device system for use in combat; however the Leo makes up for this armament's absence by having a stronger form of the Bit device known as the Pay Bit, which replicates the primary weapon of the Leo whenever it obtains a laser crystal.
The R-9 Leo is proven to be more than up to the task to destroy Major, and completes its mission successfully.
The R-9 Leo differs from other R-Crafts with notable lack of a Force Device, however despite this, the Leo makes up for the lack of the mechanism with other alternatives.
- Vulcan Cannon - a standard, semi-automatic cannon that can eliminate most small enemies easily.
- Psy Bits - a new technology unique to the R-9 Leo. Unlike the normal bit devices of most R-Crafts, the Psy Bits are capable of providing firepower to any laser-type weapon the R-9 Leo obtains, and can even fire backwards, on top of the normal contact damage and defense of the standard variant. They can also be launch to act as a diffusion-type weapon similar to the wave cannon of the R-9C War-Head. Depending on the color of laser crystal obtained by the Leo, the weapon provided by the bits will be one of the following:
- Claw Laser (Red) - fires a powerful straightforward laser, alongside an additional two smaller beams rotating around the main laser.
- Mirror Laser (Blue) - fires a large laser forward, and an additional two lasers at 45 degree angles upwards and downwards. The angled lasers are capable of bouncing off surfaces, making them useful for hitting enemies in difficult locations.
- Search Laser LR (Green) - fires five powerful lasers straightforward, which will turn 90 degrees upwards or downwards whenever an enemy is above or below them.
- Homing Missiles - obtained when the Leo collects a crystal with a "M" on it. When used, the Leo will fire two missiles that will track the nearest enemy and damage them. They have high accuracy, but deal low damage.
- Speed Up - when the Leo obtains a crystal with an "S" on it, it will increase is its overall speed by one unit for a maximum of five. One must be careful not to obtain too many, it will make the Leo harder to control.