Ever wonder how people get flawless competitively viable Pokemon in-game without hacking or cheating? It's simple; IV breeding. IV breeding uses the breeding mechanics added in Diamond and Pearl to pass on perfect IVs from a stock of parents in order to end up with a 5IV or 6IV child. It's possible in Pixelmon, although it can be extremely time consuming due to the ridiculous way breeding was implemented in the mod (revert to in-game mechanics...). Fortunately the actual breeding doesn't require your constant attention, and many servers either reduce breeding timers or provide limited access to /breed to make up for the ridiculous time breeding takes in Pixelmon.
This guide will show you how to breed flawless Pokemon from scratch. In order to get started, you need a ranch block and suitable environment (or access to /breed), a set of Power items (Weight, Bracer, Belt, Lens, Band, and Anklet), a Destiny Knot, an Everstone, and a good supply of Pokeballs. A Pokemon with False Swipe and one with the ability Flame Body or Magma Armor also help immensely. You also need a way to check your Pokemon's IVs, so this is impractical if not impossible to do on servers that lack the IVs/EVs plugin (but fortunately most servers have it).
In order to get started, you need to choose a target Pokemon and begin catching that pokemon en masse. I strongly recommend you choose a common, easy to catch Pokemon to begin with. Good starters include Magikarp, which are extremely common, evolve into the powerful Gyarados, and is a member of the Dragon egg group, allowing you to use your eventual flawless Magikarp to father other powerful Pokemon like Dratini, Bagon, and Horsea. Rattata is also a decent option, being very common in Plains and a member of the Field egg group, the largest and most diverse egg group, but is unfortunately quite disappointing in battle. When choosing a first target, make sure to take into account factors such as egg group, rarity, gender ratio, and viability in battle.
Once you choose your target, you need to start catching Pokemon of that species. Check their IVs, and discard the ones that don't have at least 1 perfect (31) IV. If you're doing a Hidden Power breed, you must substitute 30 for 31 in some stats. Use this calculator to determine what the optimal IV spread for the Hidden Power type you're after is.
You want at least 1 Pokemon with a 31 IV for each stat. So if I were doing Magikarp, I'd want one with 31 HP, one with 31 Attack, one with 31 Defence, and so on and so forth. If possible, getting a male and a female for each IV is ideal to potentially save a bit of breeding, but isn't necessary. You'll also want to find one with the nature you're looking for, but seeing as it usually takes 50+ captures in order to gather all the necessary IVs this should happen naturally anyways.
Once you've gathered your initial stock of 31 IV Pokemon, you'll need to start combining these IVs through breeding. To start with, take a male and a female with different IVs (say a Magikarp with 31 HP and one with 31 Attack) and put the appropriate Power items on them (Power Weight on the one with 31 HP, Bracer on the one with 31 Attack), and breed them together. You'll get a Magikarp with 31 Attack and HP.
Now you'll put a Destiny Knot on the 2IV Magikarp (the one with Attack and HP in this example). Destiny Knots guarantee that 5 IVs get passed on from the parent Pokemon instead of 2. Contrary to popular belief, these IVs can be pulled from EITHER parent, and destiny knots do not stack (putting a Destiny Knot on both Pokemon gives no benefit over putting it on just one). You'll then take another Magikarp with a new IV (say, the one with Defense), and put the appropriate Power item on it, then breed it with the 2IV Magikarp. It may take a couple tries but you'll eventually get a Magikarp with 31 HP, Attack, and Defence. If you happen to get one with a perfect Defense IV and either HP or Attack but not both, and it's the same gender as the one with only the perfect Defense IV, you should replace the 1IV Defense Magikarp with the new 2IV one. This is called succession, and will increase your chances at getting the next stage, a 3IV Magikarp.
Once you've got your 3IV Magikarp, move the destiny knot to it and take a Magikarp with another IV that you don't have, like Sp. Atk. Attach the appropriate Power item, and then breed them together. Like the last step, succeed the 1IV Sp. Atk Magikarp with any 2-3IV Sp. Atk Magikarps of the same gender to increase your odds at getting a 4IV. It may take several breeds but you will eventually get it.
Now that you've got a 4IV Magikarp (31 HP/Attack/Defense/Sp. Atk), I'm sure you can guess what happens next. Move the Destiny Knot to the 4IV Magikarp and put a Power item on one of the Magikarps with the remaining missing IVs, in this case Sp. Def. Breed them together, succeeding parents when necessary, and eventually you will get a 5IV Magikarp with all perfect IVs except for Speed. Again, this may take some time, but you will get it eventually. Succeeding parents will make it much faster and less RNG-based.
Now that you've got a 5IV, it's time to breed the nature. Take the Magikarp with the last remaining IV and the one with the nature you want the flawless Magikarp to have, put an Everstone on the one with the nature and the appropriate Power item on the one with the IV, and breed them. You should get a Pokemon with both the right nature AND the missing IV.
Now, put the Everstone on it and breed it with your 5IV Pokemon. Check the offspring. If it has at least 2 perfect IVs and one of them is the IV that your 5IV is missing, and it's the right gender, you replace the old parent with it. If it's the wrong gender or doesn't have the missing IV, you need to try again until you get one that is suitable. It will take quite a bit of time, but after some breeding you'll end up with 2 5IVs. If you did this step right, they should both be missing different stats (say, one with 31 in all stats except Speed, and one with 31 in all stats except HP.). Now we get to the last (and most difficult) step.
For many Pokemon you only need 5 perfect IVs. In Magikarp's case, Gyarados's Special Attack is so low that it has no business using special moves ever, so it can afford to have an imperfect Sp. Atk IV. However, if I really want to get a truly flawless Pokemon, the only way to do so is to breed those two 5IVs together. In order to get a 6IV, the breeding algorithm needs to pull 5 perfect IVs from the parents (which it has a 1 in 3 chance to do) AND generate a 31 in the last IV (which in Pixelmon it has a 1 in 31 chance to do). This results in a 1 in 93 chance to get a flawless 6IV Pokemon. This last step alone can take weeks on servers with default breed times, and usually isn't worth it unless you really need that last IV, or are willing to wait a long time to get your perfect Pokemon.
You may find yourself stuck on any one of these steps because you ended up with two Pokemon of the same gender. The solution of this is simple: take one of the Pokemon, attach the appropriate item (Everstone if it's the Pokemon that has the nature you're looking for, Destiny Knot if it doesn't and has at least 2 perfect IVs, Power item if it only has 1 perfect IV), and breed it with the opposite gendered Pokemon that has the highest amount of perfect IVs you have. Eventually you will get a suitable Pokemon with the right gender.
Gender ratio can affect breeding time significantly. For instance, Eevee has a gender ratio of 87.5% male/12.5% female, meaning roughly 1 in 8 Eevees will be female. This makes breeding take MUCH longer to complete, as succession will take on average 4 times as long as a standard 50/50 gender ratio Pokemon.
Once you've bred your first male flawless Pokemon, however, you can use it to father Pokemon that are in the same egg group, meaning you can skip the entire first part of the breeding process and move straight into breeding the right nature onto a female of your new target Pokemon, and then breeding the resulting Pokemon with your male 6IV. While practically impossible to obtain legitimately, a 6IV Ditto allows you to easily breed almost any Pokemon, including genderless Pokemon that are usually impossible to IV breed.
http://mkwrs.com/destiny_knot/ <--- IV Breeding probability calculator. NOTE: Slightly inaccurate in Pixelmon, as in Pixelmon Pokemon can't generate an IV of 0, meaning the odds of generating an IV of 31 are 1 in 31 instead of 1 in 32, as they are in game.
http://bulbapedia.bulbagarden.net/wiki/Egg_Group <--- List of Egg Groups and Pokemon in them by Bulbapedia.
http://www.psypokes.com/dex/hp.php <--- Hidden Power calculator, to determine the type and power of Hidden Power using IVs. Also shows the best possible IV spreads for any given type of Hidden Power.
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