With a heavy emphasis on story, the game takes place over the course of 16 stages with real-time and computer generated sequences intermixed throughout. Following the mission briefing you have the option to develop new weapons and equip them onto your ship. Weapons come in a few standard categories, each with its own strengths and weaknesses for particular situations.
The main gameplay portion of the game is extremely complex with hundreds of space ships on the battle field and dozens of icons on your screen at any one time. Managing all of this information is accomplished through the sophisticated Heads-Up-Display (HUD), and advanced controls. Normal flying is achieved by a combination of the left and right triggers to control speed, with the left analog stick controlling your ship's direction.
The advanced controls let you perform complicated maneuvers such as 180 degree turns, matching your enemy speed, and automatic target tracking. You also have access to a 3-level super move ranging from unleashing a barrage of missiles and shots to slowing down time to take enemies out.
Project Sylpheed is the first 3D game in the series that was originally started in the 8-bit era as a top-down shoot-em-up. This game is also the first Xbox 360 exclusive title published by Square Enix.