Pokémon Trozei!/Getting Started
Random Pokémon will fall in every level from the top of the screen (except for Pokémon pushed off the top of the screen) in random positions (although more/less equally) from any Pokémon available in the level.
Rare Pokémon will occasionally appear too, except these Pokémon will disappear after being on the bottom screen for a fixed length of time. As far as we can tell, these are also totally random, and the rare Pokémon are listed in order of rarity.
When you complete a level, you get a certain number of bonus points, depending the number of Pokémon you have left on the screen.
You also get bonus points whenever you clear the screen, 10,000 points for each time you do it. This helps you meet the stage goal and gain prize coins.
A level ends when you have Trozeied the number of Pokémon mentioned at its beginning. If, at the end of the level, you have the number of points mentioned at the beginning, you also get a prize coin. These coins are spent in the junkyard, after fighting the third boss.
Your goal, alongside rescuing Pokémon, is to fill up your Pokédex. You can get a silhouette by entering a level that a Pokémon is found in, or 'seeing' them. You can fill in that spot by catching that Pokémon.