Well I believe the ones you get are random, because there are more than 4 obtainable between all of the missions, but picking up one twice won't gain you anything. They're purple capsules that when obtained display "GET 01/00"
#1. Storm's Missions, Splash Canyon, Mission 5. It's on the 7th rail you can grind, in the middle of the waterfall.
#2 Storm's Missions, Green Cave, Mission 5. If you've hit every accelerator ring, it's floating between ring numbers 29 and 30. Otherwise, it's between ring numbers 15 and 16 after the flight ramp. It's in the area where you normally ride the centipedes.
#3 Storm's Missions, Babylon Garden, Mission 5. After the automated plane ride, while you're on the second grind rail after it you'll notice a sharp turn in the rail with another rail straight ahead which goes around a pylon thing. The manual is sitting on this rail straight ahead of you behind the pylon.
#4 Storm's Missions, SEGA CARNIVAL, Mission 5. Between the 25th and 26th accelerator rings, flying high above the ground where the NiGHTS automated track is.
If you get all 4 of these, you will have all of the manuals, but I've found some more manuals elsewhere.
#5 Jet's Missions, Extra 3, Mission 2. Right at the start of the 7th grind rail in the middle of the automated waterfall track. This is a difficult one to get right the first time becuase the rail you're on ends right before it and it makes it hard to tell it's on a separate rail, and if you miss the rail you will not pick up the manual.
#6 Jet's Missions, Extra 3, Mission 4. After the 35th accelerator ring overall, 25th after the dash panels before the automated centipede cave, it's floating in the air right before the second flight ramp in the level.
Those are all of the one's I've found, and I don't think there are any more as I've looked, but you never know. Oh, on a side note, you will get these manuals on your own if you play these missons perfectly and obtain the gold medals for them, as all of the manuals are on part of the path that you have to fly/grind to get the gold anyway.
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