Jirachi is up there with Mew, Celebi, and Deoxys. It's one of those mythical Pokémon that cannot be captured without a cheat or a rare, Nintendo-given pass. However, in Pokémon Pinball, Jirachi can be captured within the game, without cheating and without a pass of any kind.
On both the Ruby and Sapphire field, there is a button (or a Linoone) in the lower left corner of the field, right above the left flipper. Pressing this three times in a row will result in Travel Mode, in which you can travel to a different location and catch different Pokémon. After enough traveling, you'll reach the Ruins, a location only available after you've traveled so many times. There's many rare Pokémon to be found here.
Once in the Ruins, activate the start slot. You may see a strange panel on it, decorated by the word "arrival" and a white and yellow Pokémon. If you're in the Sapphire field, use Zigzagoon to pounce on it; if you're in Ruby, just time it the best you can to land on the "arrival" panel.
If you've done this, the music will change, and Jirachi will appear above the field, shimmering as he moves. You have 30 seconds to hit him three times with the ball. During this time, it's easy to panic when the time starts running down. Keep calm! Thirty seconds is more than enough time; steady your hand, and glue the sparkles in your mind so you can admire them later. =P Good luck!
Kecleon Bonus Stage
This bonus stage is in the Ruby field. It is found in the same way as the Duskull field on the Sapphire field. When all three Pokéballs in the center are filled, the start slot opens and you can play if you get the ball in it.
The field is a small section of forest, with a tree and several patches of grass. A Kecleon walks in, then turns invisible as he notices you. You can sometimes see where he is standing, when he walks over a puddle or through the grass.
To win this stage, you need to trip Kecleon by hitting him with the ball once, then hitting him again when he is on the ground. Hit him about 20 times to win.
Also, if the ball collides with the tree, a Devon Scope will fall out. Using this allows you to see Kecleon when he is invisible.
Duskull Bonus Stage
The Duskull bonus stage is found in the Sapphire field. Once you have filled the three Pokéballs under the location picture, the start slot will open. Shoot the ball into the slot, and you will be asked if you would like to go to the bonus stage.
The stage is a musty-looking graveyard, with a few tombstones and lotsa fog. There are about 20 Duskull that appear two at a time. Once you hit one with the ball, it disappears. After you get rid of all of them, the clock stops, and the ground starts to shake.
Then Dusclops materializes! Dusclops is tricky to beat. When he walks, he shakes the ground, which shakes the ball. Also, if you hit him from the front when he is standing still, he will absorb the ball and spit it out a few seconds later. Your best bet is to either wait until he walks and hit him from the front, or if you're a good shot, hit him in the back or sides. You need to hit him about 5 times to win.
Groudon Bonus Stage
Accessable on the Ruby field, this challenge is available after you have won the Kecleon stage and filled the three Pokéballs a second time.
This field is a small cave with rubies in the corners. Groudon approaches, shaking the field as he does. He falls from a higher level, knocking down several rocks as he does.
Groudon uses several different moves. He can shoot a gushing stream of fire, which immobilizes the ball temporarily if it hits. Occasionally, he will create an earthquake which knocks down barriers of rock, and he can also send up columns of flame to defend himself.
To win this challenge, you must hit Groudon about 15 times. If you can defeat him a second time, you will capture him.
Kyogre Bonus Stage
This stage is only available when you play on the Sapphire field. After you complete the Duskull stage, the next secret stage is the Kyogre stage.
This field is a small cave filled with water. Blue sapphires are set into the corners of the cave. Kyogre appears from underneath the surface of the water, and the battle is on.
Kyogre can use an ice beam that temporarily freezes the ball if it hits. He can create whirlpools that will trap the ball for a short amount of time, and he also can dive underwater where you cannot hit him.
Like Groudon, you must hit Kyogre about 15 times to win. If you can defeat him a second time, this legendary Pokémon will be added to your collection.
Rayquaza Bonus Stage
This is probably one of the hardest challenges in the game. Accessible after you have captured either Groudon or Kyogre, and beaten Kecleon or Dusclops again, you can access this stage from both fields.
You play on top of the Sky Pillar, a large tower with old, creaking floors. Rayquaza flies in, roaring, and the battle is on.
Rayquaza starts the duel with a shocking Thunder attack. It paralyzes the ball if it hits, but it takes a minute for the green dragon to charge it, so hit him then. Rayquaza can fly high into the sky, then rip through the air above the field, forming tornadoes. He also hovers above the field, making it harder to hit him.
If you are lucky or skilled enough, defeating this dragon earns you many bonus points.