The missing screens are missing frame buffer emulations. Only "FB-clear" is emulated so you don't see anything. You have to uncheck "emulate clear" box in Jabo's plugin's config to get it displayed. Also the Garbage is there and acknowledged by the emulator ('Static in cut scenes" in Plugin Notes)
This is such a good game that I cleared all levels continuously in 3 hours (one level needs appox. 45~50 minutes to beat). The best way to play this game is to use Darkman's input plugin, Perfect Dark style. you use the mouse to control the crosshair and keyboard to control the character.
The storyline (SPOILERS following) makes me believe it is a sequel to another game (dunno which). It starts with a bunch of rebels being killed by the Soldiers and the Ruffians are attacking. The protagonists (Saki and Airen) are directed by Achi (whose origin is unknown, prolly from another game) to fight the Soilders. With Achi's blood Saki transforms into a giant Ruffian (I assume) like that in Pic 6. When Achi reveals her intention to let Saki be the General of Ruffians and help her create a new earth, Saki stays wuth Airen and the human race to fight off Achi. The ending suggest the new birth of Saki and Airen's child and the beginning of a new journey (possible sequels? it would be great if true

).
Now a hint for Grahf if not already known: After you use the Darkman's plugin to conviniently control the crosshai (using mouse), ALWAYS use manual aiming mode (red crosshair) to increase your attack power.
P.S. 1964 seems to handle this game better than PJ. I noticed some effects that I don't see in PJ (clouds, water surfaces, etc.)