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Glitches in Pokémon games , both major and minor, have been a mainstay throughout the existence of the games. Glitches are reproducible errors in programs that can be either harmful or helpful. Each generation brings new glitches, and removes old ones.
Generation I (Pokémon Red/Blue and Pokémon Yellow)
When trading, if the sending end wishes to keep their Pokémon, he/she can turn off his/her game pack before the save is complete, similar to the 2nd generation clone glitch. It is unknown if there is any side effects to this glitch.
Master Ball Glitch
This glitch duplicates the items in your 6th item slot, giving you almost an infinte amount of the item, whenever you encounter Missingno. To perform this glitch, talk to the Old Man in Viridian City, who shows you how to catch Pokémon. After he shows you, fly to Cinnabar Island and surf along the East coast, on the boundary between land and water. You will encounter Missingno, a glitch in the form of a Pokémon. You do not have to catch it.
Note that this will destroy your Hall of Fame data (it shouldn't damage your saved game, though).
The mysterious coast
Using the same glitch as above, you can capture Pokémon over level 100 (they turn back to level 100 after they gain any EXP) and a wide variety of Glitch Pokémon. The Pokémon encountered will depend on your name. These Pokémon are very dangerous to the well being of your game! It is OK to attack the Pokémon or catch the Pokémon that are over level 100.
This is how you get Mew in Pokémon Red/Blue and in Yellow
Restart your game and play until you get HM02 Fly from the house west of Celadon City. You can get a Mew sooner if you use teleport from the nearby Abra, the easiest way is to start leveling a Jigglypuff so its sing is faster then the Abra's Teleport.  DO NOT fight the following trainers:
1) The Youngster with a Slowpoke (Level 17) on the road to Bill's house (Route 25). He is the fourth trainer after you cross Nugget Bridge, standing directly above a female trainer and facing north (If done before battling Misty, the first swimmer in her gym, his last Pokémon will be Horsea).
2) The Gambler with two Poliwags and a Poliwhirl (all Level 22) between Lavender Town and Saffron City (Route 8). He is standing just east of the entrance to Saffron City, facing north toward the door of the Underground Path (or the man standing in the grass at the very left of Cerulean Cape. Using him instead of the Gambler means you can do this before the second gym).
3) Carefully follow the series of steps illustrated below:
Make sure you have a Pokémon that knows Fly. On Route 8, stand in front of the door of the Underground Path. Save your game, since saving after this point will disrupt the procedure. (If at Cerulean Cape stand above and one step left of the water.)
Walk down one step and immediately press Start. If you succeed, the menu will pop up before the Gambler "sees" you. Go to the Pokémon list and fly (or teleport) to Cerulean City (same for the Cerulean Cape trainer).
The Gambler will see you just before you fly away.
Your Start button will no longer function. Go north across Nugget Bridge and head east until you find the trainer in this picture (he's the Youngster described above).
If you walk right up to the Youngster, the game will freeze, so you'll have to let him see you and walk up to you. Defeat his Slowpoke (afterwards, your Start button will work again), then fly to Lavender Town. If you want to have a level 100 Mew right away, use the move Growl on the Slowpoke exactly six times before defeating it.
Head west into Route 8 (if done using the Cerulean Cape trainer instead of the gambler, head up onto Nugget Bridge).
As soon as you enter the narrow path, the menu will pop up by itself. Press B to exit on Nugget Bridge, the start menu will come about halfway up.
Look who it is! Mew will be at Level 7 and its only attack will be Pound. If you used Growl on the Slowpoke or Horsea six times, the Mew will only be Level o1.
Once you've caught Mew, you can save your game without any ill-effects. If you use a different trainer then the Slowpoke trainer you can get different Pokémon, although Mew would probably be your most valuable since you can teach him any move.
If you got the Mew at level one, take it into a battle and make sure it gets less than 58 exp. If it gets over 58 exp, it will level up to level 2, but if gets less than 58 exp, it levels straight to level 100. It will only know Pound so you need to teach it other moves through TMs.
There are two alternative ways to enter Route 8 and trigger Mew after beating the Youngster. If you have access to Saffron City, you can fly there and go through the eastern city gate. Also, you can fly to Celadon City, head east to Route 7, enter the Underground Path, and emerge back in front of the Gambler.
Finally, the Route 8 Gambler isn't the only trainer that can initiate the trick. The Super Nerd just west of him can also do it, as can the second Fisherman you meet when heading south from Lavender on Route 12. There are numerous others; basically, any trainer who is scrolled onto the screen by the same step that puts you in their vision range will work. However, remember that the final battle with Mew will only be triggered by returning to whatever route that trainer is in, which is not necessarily Route 8.
Man Walking on Roof
Use the move surf on the east coast of Cinnabar island, then land directly in front of Blaine's Gym, the man wandering in the street will appear in the roof of the gym and then go down when you make a move.
Standing on a Bush
Cut down a bush with Cut and move to the spot where it was standing. Save the game and turn it off. When you turn it back on, your character's sprite will be directly on top of the bush.
Enter the Safari Zone, and then immediately try to leave. When asked if you want to retire early, say no. When you re-enter the Safari Zone, save your game and turn it off. Turn it back on, and try to leave again. You will be asked if you want to purchase time in the Zone. Say no, and leave the building. Fly to any town and walk around. After 500 steps, you will hear the end-chimes and be back in the Safari Zone entrance. When you leave the building again, you will be in "Glitch City."
Make sure that you do not save the game, or make sure that you have a Pokémon that knows Fly. Otherwise, you will not be able to leave Glitch City.
Generation II (Pokémon Gold / Silver and Crystal)
Go to a computer and have the Pokémon you want to clone in your party. Save the game directly in front of the computer (to make it easier as doesn't actually help the glitch) and deposit the Pokémon into the PC. Start to save the game, but right after the scrolling text finishes with some text like "saving game do not turn off the power". immediately turn off the power (before the save finishes). When you re-enter the game you should have a copy in your PC and the original in your party.
1. Some times the Pokémon will have no name in the computer and its name will be ? else where, the Pokémon still works fine.
2. (less often) your Pokémon will have the skills and name of another Pokémon in your pc box, but still have the same image as the original.
3. (even less often) You get a bad clone, ? name and level 0. if you really want to play it, take it to the day care lady because a lvl 0 or lvl 1 can not actually battle in the game.
4. (very rarely) Your original Pokémon gets deleted, it's pretty rare that this happens but theres a chance that it could. It's believed it is usually caused by turning off the power at the wrong moment. This glitch is also often used to duplicate rare items, giving a Pokémon a Rare Candy or Master Ball before cloning results in 2 copies of the Pokémon, each holding the designated item.
Generation III (emerald only)
to clone a pokemon in emerald, once you have made it to the battle frontier, go to the Battle Tower and on the far right there is a pc. open the pc and put four pokemon you want to clone in an empty box then exit the pc and save the game. after you save the game take out the four pokemon and go directly to the lady standing at the link multi battle rooms (the lady on the far right). chose two pokemon to be enterd (so you must have more than one elligable pokemon for battle). and turn the power off when you are saving the game.
next turn the game on and you will have the four pokemon in your pc and the four pokemon in your party...
if you chose more than four pokemon the last pokemon you chose will be deleted instead of cloned.
Pokémon Cloning - Exploit
Not so much of a glitch as a flaw in the design of the game that allows a user to exploit it and clone "Legit" Pokémon without action replay or gamesharks.
It does however require a R4 or one of the various other Flash carts.
It requires a Homebrew Application called 'NDS Backup Tool Wi-Fi' Basically you are required to set up a FTP server on your PC
"smallftpd" is perfect, set it to port "8080", Tick "Use Local IP", set up a user with User/Pass as "Admin" "Admin" then under directories put in "C:\TempDS" (You will need to create that folder) Also note that in Windows Vista without permission things will be prevented from writing to the C Directory so if you have a partition use that.
Under Permissions put LRW (Listen, Reading, Writing) and save that user. Then Click the Server tab and hit "Save config" then press the play button.
Now in the 'NDS Backup Tool Wifi' You will find a config file open it in notepad and edit the specific parts needed, EG Port to 8080, User/Pass to Admin/Admin and IP of your computer which can be obtained from Comand prompt by typing 'ipconfig'.
Save that and load it on to the R4, Make sure your DS has the current Wi-Fi settings correct. Run the Homebrew application and it will search for a connection then it will show you that it's done by asking you to put in the game cartridge (Pokémon Pearl/Diamond) then you will know its worked if it has the title of the game etc.. now navigate till it has "Back up SAVE" and Begin the process. Now on your PC you'll have an exact copy of the save file from your game cartridge.
Now restart the DS and load the game, go in game and trade off all the Pokémon you wish to "clone" might as well get them to hold expensive items and then turn off your game, reload the R4 and repeat the process but this time navigate to "Restore SAVE" and restore the SAVE file you made earlier.
If all successful when you load Pokémon up and log back in you will have all the Pokémon as well as your friend. This DOES NOT work currently for Pokémon HeartGold or SoulSilver as they use a new cartridge type and NDS Backup Tool Wifi doesn't recognise the save type.
This requires 2 Pokémon Black or White games, C-gear, a Pokémon you are willing to get rid of(on one game), and a Pokémon you want to clone(on the other). First, make sure the C-Gear is turned on on both games. Then, use the trade option. Trade the Pokémon you want to clone with the one you want to get rid of. The person who is recieving the Pokémon you don't want should turn off the game without saving after the trade is complete and the C-gear has been turned off. The other should save as soon as the trade is complete. Then, both people will have the Pokémon that was cloned.