Magic Ninja Guide

Stats
To start off, your initial stats should be:
Str:1
Agi:5
Vit:1
Int:9
Dex:9
Luk:5

Your final stats should look something like this:
Str:1
Agi:5
Vit:50
Int:99
Dex:80
Luk:5

Int
Every 5 int, you get a a bonus to your max Matk. Every 7 int, you get a bonus to your min Matk. With the best +int gear, you should be able to hit 120 int (without bless). At higher lvls, dropping even 1 int could mean losing roughly 50 Matk. While 50 Matk doesn't seem like a lot by itself, it gets multiplied by 900% from Exploding Dragon to 450 damage. 900-1800 damage if the target is lexed/weak to fire.

Dex
As for dex, you really don't need to max it since most ninja skills have a very low base cast time. You can make up a lot of it through +dex equipment. However, higher dex does make a difference in long casts such as lvl 10 Freezing Spear or lvl 5 First Wind.

Vit
Vit is very important since Ninjas are rather squishy. The main purpose of this is to increase your max hp so you don't die instantly in PvP. A sinx's Soul Destroyer can do, on average, about 5k damage even with Cranial, Beret, and Immune. At lvl 99 with only 1 vit, you will only have about 4.1k base hp. In contrast, if you have 50 vit, you will have 6.1k base hp which is more than enough to survive most SD's.

Skills
Flip Tatami:
This skill allows you to block all ranged attacks for 3 seconds, similar to a priest's Pneuma. This includes Soul Destroyer, Acid Bomb, and Falcon Assault which are the main killers of Ninjas. However, it does come with a catch: For those 3 seconds, you may not move or attack in any way. Technically, you can move, but if you do, you will no longer be under the tatami's protection and you will still have the aftercast delay. Although you are essentially immune to all ranged attacks, you are a sitting duck for melee/magic attacks.

Shadow Leap
This skill has a lot of use in both PvP and PvM. However, a hide accessory is required to use it. It's main use is to leap out of range when being chased and escape. It does have a 1 second aftercast delay after use, so you can't keep spamming it unlike a Taekwon's Leap.

Note: Contrary to iRO's description of Shadow Leap, it currently does not ignore obstacles in the way. However, in some maps (particularly the old ones) you can hop cliffs. The rule seems to be that if you can snipe from the cliff, then it is leapable.

Cicada Skin Shed (CSS)
This is the defining skill of the Ninja class. It allows the ninja to dodge almost all physical attacks and at the same time, be pushed back 7 spaces. There are both pros and cons of this. The pros are that they give you plenty of time to cast your skills. While you have CSS on, your cast will not be interrupted when hit by a physical attack. The movement also maintains your range, forcing the enemy to struggle to catch up to you. The cons are that if you get too close to a wall, you may be trapped against it as the enemy attacks you. Try to use CSS only in open areas and avoid walls. Also note that while it makes you nearly invincible to physical attacks, it does nothing to block magic attacks and certain skills.

Lvl 3 CSS is the minimum you need for efficient leveling/pvp since it blocks 2 attacks before you need to recast it again. Some people max it to lvl 5 for the extra dodge, but this is based on personal preference.

List of "physical" skills that pierce Cicada Skin Shed:
Acid Bomb (Biochem)
Soul Destroyer (SinX)
Falcon Assault (Sniper)
Excruciating Palm (Monk)
High Speed Cart Ram (Master Smith)
Venom Knife (Sin)
Stone Fling (Sin, Rogue)

Ninja Aura
Although +5 int may not seem like much, at higher lvls it will add about 50 Matk. This skill should be saved for last since it doesn't do a lot at low lvls. With this skill and full +int gear, it is possible to reach 125 int self-buffed and 135 int with bless (950 max Matk).

Flaming Petals
This skill should be gotten early on to help with leveling. I stress however, that you will not need to have it over lvl 5 since Exploding Dragon will be far superior to it. However, if you can remember to skill reset before you hit Base lvl 40, lvl 10 is helpful for early leveling.

Blaze Shield (BS)
Blaze Shield is a great tool for both leveling and WoE. When leveling, all you need to do is cast Blaze Shield and drag a monster into it with lvl 1 Freeze Spear. Each cell it touches will hit it multiple times depending on the skill lvl. One tactic is to drag it in a line similar to a Mage's vertical firewall so that you can keep track of it more easily. Also, instead of watching the monster, watch the cells under it as they disappear so that you can time when you need to move.

Note: Monsters with very high movement speeds (Rideword, Mimic) will skip right through this and take little damage. In WoE, it is one of the few skills in the game that stalls movement when inside a castle. Because of this, it is a better alternative over Watery Evasion when defending.

Exploding Dragon (ED)
Exploding Dragon is the most damaging skill a Ninja has. When used, it hits everything in a 5x5 area around a targeted enemy. This makes it a great leveling skill when mobbing. However, while it does massive damage with a short cast time, it does have a 3 second after-cast delay so make sure CSS is activated prior to using it.

A trick you can use is if you can keep a target moving at the time that ED is cast, it will actually be hit twice (6 total hits). In the time that the animation for ED lasts, every cell in a 5x5 area around the monster will hit 3x. This is easier to explain if you imagine ED to be a Blaze Shield that lasts for only 1 second. If you time it right with CSS, the monster will run through 2 cells and take two times more damage than if it were standing still. I am not sure if this works on players, but I know that it does work on Homunculus. One ED is usually enough to kill a Homunculus if it is moving.

Freeze Spear
Freeze Spear has the fastest cast time of any Ninja skill. It also has no aftercast delay so it is one of the most spammable skills in the game. Lvl 1 hits three times per cast so it is great for stalling people in PvP. It also prevents someone from Hiding/Cloaking if you continue to spam it on them.

Note: Although the skill description says each hit will only do 70% Matk damage, it actually does 100% Matk damage per hit.

Watery Evasion
Watery Evasion is a very useful skill in both PvP and PvM. In PvM, it is used to slow large mobs down so that you have more time to cast. Also, this is the only skill in the game that can slow down MVPs so make sure to use it when MVPing. In PvP, it can be used to slow players, although Blaze Shield is a better alternative. It is also much more cheaper to use than a Sage's Deluge so you can spam it to allow a wizard to use Waterball. If you are not planning to get Snow Flake Drift, lvl 4 provides a large enough range for practical use.

Note:Contrary to what it says in iRO's skill description, it currently does not increase the damage of Freezing Spear.

Snow Flake Drift
In my opinion, this skill is not worth getting. Snow Flake Drift is almost exclusively a PvP skill. At max lvl, it only has a 60% chance to freeze, as opposed to a wizard's 100% chance from Storm Gust. Subsequent casts will also not damage frozen enemies. The range of the skill is dreadful and is only made worse by its long cast time. If you get knocked back by CSS before you finish casting it, it will miss. Although the skill sounds great in concept, it is not very good in practice.

Wind Blade
Wind Blade is used on monsters that you cannot use fire/water on (water property monsters i.e. biblan, ice dungeon). There is no difference between lvl 4 or lvl 5 other than sp costs so stick with using lvl 4. The only reason to get lvl 5 is to get Lightning Jolt.

Lightning Jolt
Lightning Jolt is similar to Snow Flake Drift in that it does mediocre damage and has a small range. The only difference is that it doesn't have an after cast delay so it can be spammable. This should only be gotten if you plan to get First Wind.

First Wind
First Wind is great for leveling in ice dungeon and on water monsters. It has the potential to do more damage than ED in PvP/WoE since it has no aftercast delay. Since it is wind element, its damage is not reduced by Valkyrie Shield and also does more damage to people wearing Aqua armor. Although it is not technically an AoE, it does have enough range to hit everyone at a choke point in WoE.

Skill Build
1 Flip Tatami
5 Shadow Leap
5 Cicada Skin Shed (CSS)
10 Ninja Mastery
5 Ninja Aura
5 Flaming Petals
7 Blaze Shield
5 Exploding Dragon
7 Freeze Spear
4 Watery Evasion
5 Wind Blade
5 Lightning Jolt
5 First Wind

Order in which to get skills:
1 Ninja Mastery
1 Freeze Spear
5 Flaming Petals
5 Blaze Shield
1 Flip Tatami
5 Shadow Leap
3 CSS
7 Blaze Shield
10 Ninja Mastery
5 Exploding Dragon
5 CSS
5 Wind Blade
5 Lightning Jolt
5 First Wind
5 Freeze Spear
4 Watery Evasion
5 Ninja Aura
7 Freeze Spear

A good skill build doesn't have to exactly match mine, since you can take out some points from Freeze Spear or Ninja Aura and put it elsewhere. It's really a matter of preference.

Leveling
Lvls 1-12 (Novice)
Do Novice Training grounds to get up to job lvl 7.
You should be able to kill Spores/Poporings solo even without gear (as long as you have Novice Red Pots) until job lvl 10.

Lvls 13-22 (Ninja)
Spores (1 south of Payon)
Poporings (1 south, 1 east of Prontera)

Lvls 22-30
Wolves (2 south of Payon)
Metalings (1 north of Einbroch)

Lvls 31-60
Drosera (1 east, 1 north, 1 east of Rachel)
Mi Gaos (Louyang)
Groves (1 south, 1 west of Hugel)

Lvls 61-70
Clocks (Clock Tower lvl2)
Alarms (Clock Tower lvl3)
Stings (southern GH entrance, 1 east, 1 west, topright warp of sewers)
Zombie Prisoners, Skeleton Prisoners, Injustices (GH Prison).

Bring fly wings or teleport belt to avoid Mimics/Ridewords/Gargoyles.

Lvls 71-90
Stalactic Golems (1 north of Comodo)
Vanberk, Isilla (Rachel Sanctuary lvl1)
Hill Winds (1 east, 2 north, 1 east of Rachel)

Lvls 90-99
Stalactic Golems (1 north of Comodo)
Ice Titans, Snowiers (Ice Dungeon lvl3)
Galions (1 east, 2 north, 1 west of Rachel)
Hill Winds (1 east, 2 north, 1 east of Rachel)

Equipment
Ninjas aren't really gear dependant but the basics that you will need are:
Ashura[3]
Sohee Shoes
Hide Accessory
Heal Accessory
Teleport Accessory
Hard Armor

Ninjas also have the ability to create Ninja-only shields (Arm Guards) inside the Ninja Guild. There are 3 npcs inside, each creating a different shield. They will only talk to you if you are a Ninja.

Arm Guard [1]
Def: 5
Ingredients: Guard[1] + Arm Guard
(Bought from Ninja Guild)

Advanced Arm Guard

Def: 4, MDef: 5
Ingredients: Mirror Shield
(Bought from Geffen Armory) + Arm Guard
(Bought from Ninja Guild)

Advanced Arm Guard [1]
Def: 4, MDef: 5
Ingredients: Buckler[1] + Advanced Arm Guard
(Created in Ninja Guild)

Full Dex Gear (+14 Dex):
Mid Headgear: Erudite Sunglasses
Headgear: Apple of Archer
Garment: Immune Muffler
Accessory: Nimble Glove
Accessory: Nimble Glove
Weapon: 3x Dextrous Ashura
Armor: Hard Armor
Shoes: Sohee Shoes
Shield: -30% damage vs race Advanced Arm Guard

Full Int Gear (+16 Int):
Mid Headgear:Erudite Sunglasses
Headgear: Morpheus Hood
Garment: Morpheus Shawl
Accessory: Morpheus Bracelet
Accessory: Morpheus Ring
Weapon: Bazerald
Armor: Hard Armor
Shoes: Sohee Shoes
Shield: -30% damage vs race Advanced Arm Guard

With Full Int gear, you can achieve well over 1k max SP.