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Dear lord I've been trying to catch the damn thing in Pokemon HeartGold for way too long! I've looked up all kinds of tutorials and videos and what not but it is just not happening and I'm honestly afraid I'm gonna break my start button from soft resetting so much -__-' .... Anyways, my question is this; HOW do I catch it? Or how best to catch it, is there a trick? a better pokeball?

Oh, and heres the catch... I've transferred virtually every Pokemon from this game to Pokemon y. all I have left are the following Pokemon and I'm really only trying to catch the damn legends to fill my PKMN Y pokedex so I'd like to spend as little more time on them as possible. So, here are the pkmn I have left (other then the other legends, I have none of them yet).

*Pidgot: Lv 47
Fly
Roost
Wing Attack
Quick Attack

*Kyogre: Lv 50
Aqua Ring
Ice Beam
Ancient Power
Water Sport

*Kingler: LV 40
Metal Claw
Rock SMash
Surf
Cut

*Machop: Lv 12
Low Kick
Rock CLimb
Focus Energy
Karate Chop

*Groudon: Lv 50
Cut
Earthquake
Ancient Power
Eruption

*Krabby: Lv 23
Surf
Whirlpool
Bubblebeam
Mudshot

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Put it to sleep or paralyze it, things become easier from there. Although you don't have anything that can do so, you might wanna get something that can. Preferably an Electric type than knows Thunder Wave.
Try using one of the best pokeballs in the game for catching legendaries that some people are mad that it didn't make it to the games after Gold/Silver- the Heavy Ball

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Best answer

If the following is what you're doing already, then unfortunately there's no easier way to do it. Doing all of the following results in the highest capture rate possible for Rayquaza in Gen 4 (7.095% chance per ball), so you'll have to keep chucking balls at it. If you aren't doing this, great! This'll help you out a bit.

  1. Freeze it or put it to sleep. Sleep is much easier as it can be induced without relying on luck. Use a move like Sleep Powder on it to put it to sleep. You can also give it any other status condition, but sleep and freeze increase your chance more. DON'T burn or poison it, as it will kill itself eventually.
  2. Use False Swipe to lower it to 1 HP. False Swipe is a TM and lots of Pokemon can learn it (including your Kingler), so you should have no problems with this.
  3. Play at night and use Dusk Balls. Dusk Balls have the highest capture rate of all at night or in a cave. I'm not sure Embedded Tower counts as a cave (if it does ignore the part about night time), but make sure you are playing at night just in case. If you can't, Ultra Balls are the next best balls to use. Your chance per ball will be closer to 4% if you do this though.

After you've got this done, keep throwing balls at it. As stated before, each ball has roughly a 7.1% chance of capturing Rayquaza. According to the calculator below, you have at least 95% chance of capturing it within 41 balls.

The chance is so low because Rayquaza's base capture rate is 3 in Gen 4 (the lowest capture rate in the game). As of OR/AS, it's 45, which gives you much better odds.

Capture rate calculator

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Well damn, I was afraid of that lol. Thanks a bunch! You did gimme a few extra pointers I hadn't thought of.  I guess all I can do now is just thy the above, keep wingin' pokeballs at it and keep my fingers crossed!