PokéBase - Pokémon Q&A
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In general, there is a small random chance of capturing a boss Pokémon. When a Pokemon is wobbling, it will have yellow stars coming out of it, and will spin. The wobble effect lasts for about 5-10 seconds. When the Pokemon is wobbling and you're able to defeat it while it's wobbling, it will be a 100% guaranteed capture.

If you're trying to catch boss Pokémon or any Pokémon, you should read this:
Just ignore the part about modes if you want normal Pokémon.

Imagine the game works like this: You spin a prize wheel and whatever it lands on (coins or the Pokémon), that's what you get. If you need some coins you could just do the opposite of what my info says.
I hope I solved your problems, if not, comment on my answer.

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The game does have a prize wheel though. That's why it's good to slow down time for 2 diamonds so it lands on what you want.
Hwo do you get it to wobble?
>Boss Pokémon have three "modes".
First Mode (Normal) --> No smoke coming out of the Pokémon. Normal stats, simple attacks. This is how you will encounter the Pokémon when you first enter the boss stage.
Second Mode (White Smoke) --> After the Pokémon has attempted to make three attacks in the normal mode, it will be in White Smoke mode. The Pokémon is charging to make a "blast" attack. (If you attack the Boss Pokémon in "Normal Mode" too much, it will skip straight the black smoke mode).
Third Mode (Black Smoke) --> 50% more speed and 50% more attack. It's recommended you run when it's in Black Smoke mode.
To make the Pokémon wobble, you will need to spam attack it while it's in White Smoke mode (This works for other Pokémon, but not with the smoke).
Do not switch out Pokémon when the Boss is wobbling as it will get rid of the wobble effect. You will need to use the same Pokémon you used to make it wobble, to defeat it.
- Making the Pokémon wobble won't always work. Which is why it is important to have a high level Wobble Tree.
- Dragon Claw can be taught to most Pokémon from the Move Tutor Shop, so it's probably the easiest spam move to obtain.
- Using a high power Gutsy Pokémon increases the chance of making the Pokemon wobble.
Normal moves can make a Pokémon wobble too.