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Due to the use of late game topics, spoilers as follows.

I want to see how quickly I can kill the Doctor, and I want to get enough missiles to destroy both forms of him. Through the game, I came across enough missile max upgrades to get it to 25 (only got 20, skipped the zombie sky dragon one). Are there any other ones I can collect, and if so, where are they?

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There are 5 missile expansions that bring you up to a grand total of 54 missiles. The first 4 on this list give you 5 missiles each, while the last "Bonus" upgrade gives you an additional 24.

Grasstown

Right above the building with the motorbike outside/door that needs to be destroyed by a bomb.

Grasstown

Inside the grasstown hut just above the shelter where Kazuma was locked in.

Egg Corridor

After returning to Egg Corridor. By the sky dragon in where egg 12 used to be.

Egg Corridor

After returning to the Egg Corridor. Inside the Egg Observation Room

Bonus Missile Expansion

Located in the Sacred Grounds secret stage in a chest hidden in a single star block located high on a ledge just before the room with Heavy Press boss fight.

Source: http://wikicheats.gametrailers.com/Cave_Story_-_PC/Max_Missile_Expansion_Locations

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