A-GA - Gekidou no Wakusei

Hidden Cutscene:
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On the extra page, you may finish the game and find you have a cut
scene missing; the movie selection picture is located on the bottom
left hand corner of the screen. This is unlocked by losing to the final
playable boss (the one with giant shoulder cannons and the bandaged face;
he occurs in the story after the pipe organ puzzle but right before the
colored bubbles puzzle) and selecting "NO" when asked to continue. 

Unlocking this cutscene will reveal the fate of Eo and her friends against
the monster's many tentacles. 

Fighting Boss Battles:
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Fighting bosses in this game is a snap. Just remember to use your entire
desk to sweep the mouse from left to right and vice versa; dont' confine
your arm movements to your mouse pad. This way you can jump from one end
of the room to another while firing without ever having to stop and reset
the mouse position . 
You can also use the right mouse button to re-aim your weapon elsewhere 
but if you use this strategy you honestly won't need to do so.

Solution to Pipe Organ Puzzle:
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To unlock the first door play "mi, la, si, la, re, si, re, so" as written
on the keyboard. To unlock the second door play "so, si, si, si, so, la, 
re, do". Note that you must get the keys for this in order to use the pipe
organ.

While this is very apparent in the game, this may be difficult to understand
if you don't speak Japanese. 

Solution to the Colored Bubble Puzzle:
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After defeating the final playable boss, you will come to a room with locked
doors and a machine that spits out colored bubbles. Collect the bubbles in 
this order to advance: white, red, red, green, yellow, white, blue and blue.