What is the best way to capture legendary Pokemon?

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Before doing anything else, throw a Quick Ball. The first turn chance is always worth a shot.

Send out a good catching Pokemon. This means something that has False Swipe, and can inflict a status condition. Things like Gallade and Bisharp are good choices.

Whittle down the Legendary’s HP with False Swipe, until it is at around 1 HP.

Inflict a status condition, preferably Sleep or Paralysis, as those cannot hurt the Legendary the way Poisoning and Burns do.

If the Legendary is in a dark place, or it is nighttime, throw Dusk Balls until you catch it, or the status condition you inflicted wears off.

If it is not in a cave and it is daytime, use Ultra Balls instead until you catch it, or Repeat Balls if you somehow managed to have the Legendary Pokemon before.

Enjoy your newly-caught Legendary.

Alternatively, just throw a Master Ball at it and save yourself the hassle. Also note that if the Legendary has a recovery move, make it a priority to inflict the status condition first, as that can cripple it, and may prevent it from using its recovery move.

Hope I helped!