EDIT: Shifted around the levels at which certain abilities are gained. Added Spot prerequisite. Replaced Ninja Sight with Gez's Nightprowler ability, marginally tweaked. Lessened Fast Movement, base Fortitude save, spellcasting progression, and Trap Sense progression for the sake of balance, considering the class' spellcasting ability in addition to all its other capabilities. Should be reasonably balanced with the core assassin prestige class now, or close enough.
Lessee, seems that what he's going for is a ninja assassin who slips in, causes some brief carnage, then slips out before any organized response can be thrown against him. Emphasizing two weapons, double weapons, and throwing weapons for offense, using surprise, stealth, and trickery to cause the carnage, not really meant to stick around and duke it out with a prepared foe. Here's my quick thrown-together version, which is probably somewhat overpowered in its first iteration, due to the spellcasting ability:
NINJA ASSASSIN (or SHADOW WARRIOR)
Prerequisites: Dodge, Mobility, Quick Draw, Point Blank Shot, Spring Attack, Throw Anything, BAB +5 or greater, Balance 8+ ranks, Bluff 8+ ranks, Climb 8+ ranks, Disguise 8+ ranks, Hide 8+ ranks, Jump 8+ ranks, Move Silently 8+ ranks, Spot 8+ ranks, proficiency in all martial weapons, Evasion.
HD: d6
Alignment: Any nongood (or whatever works for how you integrate it into the campaign)
Class Skills: As rogue
Skill Points At Each Level: 4 + Int modifier.
The Ninja Assassin
Level_BAB__Fort_Ref_Will_Special
1____+0___+0__+2__+0__Spells, Paired Weapons, Nightprowler (basic, 1/day), Trap Sense +1
2____+1___+0__+3__+0__Improved Throw, Skirmish +1d6, Poison Use
3____+2___+1__+3__+1__Hide In Plain Sight, Fast Movement +10 ft.
4____+3___+1__+4__+1__Skirmish +1d6/+1 AC, Nightprowler (improved, 2/day)
5____+3___+1__+4__+1__Paired Weapon Flurry, Fast Sneak, Trap Sense +2
6____+4___+2__+5__+2__Fast Climb, Skirmish +2d6/+1 AC
7____+5___+2__+5__+2__Opportunist, Power Throw, Nightprowler (greater, 3/day)
8____+6___+2__+6__+2__Skirmish +2d6/+2 AC, Slippery Mind
9____+6___+3__+6__+3__Run On Walls, Trap Sense +3
10___+7___+3__+7__+3__Paired Weapon Mastery, Nightprowler (perfect, 4/day)
Weapon And Armor Proficiency: The ninja assassin gains proficiency in all weapons a monk is proficient in.
Spells: Ninja assassins learn a smattering of arcane techniques to aid in their stealth and trickery. Thus, a ninja assassin casts spells as per a bard, with certain exceptions. Thus, their spellcasting is based on Charisma, is arcane, always requires a verbal component, is spontaneous, and ignores arcane spell failure from light armor but not from other armors or shields. A ninja assassin's spells known and spells per day, however, are as per the assassin prestige class, with an effective assassin level equal to their level in this class for purposes of spellcasting. They choose their spells from the bard's spell list. Do not, however, stack these levels with actual bard or assassin levels; a ninja assassin's spellcasting is separate.
Paired Weapons: At 1st-level, the ninja assassin learns a martial arts style for wielding various weapons in a combination offensive. Thus, when wielding any special monk weapon, or a quarterstaff or two-bladed sword, the ninja assassin gains the benefits of the Two-Weapon Fighting feat if he does not already have the feat. If he does, then instead he gains +1 on weapon attack rolls and damage during any full-attack action where he attacks only with these weapons. The damage bonus is multiplied normally if a critical hit is scored. Paired Weapons only applies in light armor or no armor.
Nightprowler (Su): Ninja assassins develop a keen ability to see in the dark, learning a special ki technique to enhance their sight in dark or dim conditions. Nightprowler is a supernatural ability useable once per day, plus an additional once per day per 3 levels in the class beyond 1st (2/day at 4th-level, 3/day at 7th, and 4/day at 10th). Activating Nightprowler is a full-round action that requires concentration (thus subject to distractions, as per casting a spell, but it does not provoke an attack of opportunity, and losing concentration only prevents that attempt from working, it does not waste that daily use). Activating Nightprowler requires a successful Spot check against DC 20, and failing the check does not waste that daily use, but a failed check does prevent the ninja assassin from attempting Nightprowler again for 1 minute; the penalty for failure means a ninja assassin cannot take 20 on this check.
If Nightprowler is successfully activated, it functions for 1 minute per level in the prestige class. After a successful use of Nightprowler is complete, the ninja assassin must rest his eyes for half a minute (5 rounds) before attempting to use it again, or else his eyes become strained and he suffers a -4 penalty on any sight-based checks or rolls, including attack rolls. If they don't rest their eyes for half a minute before attempting Nightprowler in these circumstances, they also treat foes as though they have half concealment (or full concealment if already possessing half concealment), which is not reduced by any abilities or effects upon the ninja assassin. Such penalties last until the ninja assassin rests his eyes for 1 minute (10 rounds).
When Nightprowler is successfully activated, it grants low-light vision, stacking with any existing low-light vision. As normal, two doublings is a tripling, a doubling and a tripling are a quadrupling, and so on, in cases of stacking low-light vision.
At 4th-level onward, a second Spot check may be attempted when Nightprowler is activated, against DC 25. If this second check is successful, the ninja assassin also gains darkvision with a range of 60 feet, or adds 60 feet to their existing darkvision, if any.
At 7th-level onward, the ninja assassin can attempt a third Spot check when activating Nightprowler, against DC 30. A success grants the ninja assassin a further +90 feet to the range of their darkvision, and improves their low-light vision one degree.
Lastly, at 10th-level onward, a fourth Spot check can be attempted with Nightprowler when it is activated, this one against DC 35. A success allows their darkvision to piece even unnatural darkness, such as from a Darkness spell, and also allows the ninja assassin to see invisible and ethereal creatures with their darkvision.
Failing the first Spot check prevents attempting the other Spot checks for Nightprowler, while failing the second Spot check prevents attempting the third and fourth, and failing the third Spot check prevents attempting the fourth. The ninja assassin has no other drawbacks for failing the additional Spot checks for Nightprowler, but they still cannot take 20 on these Spot checks.
Trap Sense: As per the rogue ability.
Improved Throw (Ex): As an extraordinary ability, ninja assassins of 2nd-level or higher add +10 feet to the range increment of anything they throw, including improvised thrown weapons. Also as part of this ability, they gain +1 on attack rolls with thrown weapons, even improvised ones. Lastly, during any full-attack action where the ninja assassin only attacks with thrown weapons, he may make one additional throwing weapon attack during that action, at half his base attack bonus, rounded up. In the case of shuriken, three can be thrown with each attack, even this extra attack, as normal.
Skirmish: As per the scout or peregrine runner ability.
Poison Use: As per the assassin ability.
Hide In Plain Sight: As per the shadowdancer ability.
Fast Movement (Ex): Ninja assassins of 3rd-level or higher move with great haste to accomplish their tasks and escape before any retaliation. In light armor or no armor, while carrying no more than a light load, the ninja assassin adds +10 feet to their land speed. Fast Movement is an extraordinary ability.
Paired Weapon Flurry: At 5th-level the ninja assassin's special fighting style develops further, and he gains the benefits of the Improved Two-Weapon Fighting feat with the weapons mentioned in the Paired Weapons description. If he already possesses the feat, he instead gains a further +1 on weapon attack rolls and damage during any full-attack action where he attacks with only those weapons. The damage bonus is multiplied normally if a critical hit is scored. Paired Weapon Flurry only applies in light armor or no armor.
Fast Sneak: As per the ninja of the crescent moon ability. Functions only in light or no armor, and carrying no more than a light load.
Fast Climb: As per the ninja of the crescent moon ability. Functions only in light or no armor, and carrying no more than a light load.
Opportunist: As per the rogue ability.
Power Throw (Ex): A ninja assassin of 7th-level or higher has perfected their mighty throwing techniques. Increase the base damage of any material object the ninja assassin throws, by one step in damage dice. A base of 1 damage becomes 1d2, 1d2 becomes 1d3, 1d3 to 1d4, 1d4 to 1d6, 1d6 becomes 1d8, 1d8 becomes 1d10, 1d10 becomes 1d12, 1d12 shifts to 2d8, and 1d20 shifts to 2d12. If the base damage is multiple dice, increase each die one step along this progression. Also, the ninja assassin now adds their Strength modifier as an additional competence bonus on damage rolls with such weapons. These benefits even apply to shuriken. The ninja assassin now ignores half the normal penalty on attack rolls for throwing weapons beyond one range increment. Power Throw is an extraordinary ability.
Slippery Mind: As per the rogue ability.
Run On Walls (Ex): A ninja assassin of 9th-level or higher is so swift and so deft at controlling their center of gravity through ki that they can move along walls, and even ceilings, for a few moments. During any run, charge, partial charge, or double move action, the ninja assassin can use their Run On Walls extraordinary ability. As long as they begin their movement on a surface they could normally walk along, and as long as they actually move at least 10 feet along such a surface, the ninja assassin can move along walls and ceilings during any run, charge, withdraw, or double move action.
However, they can only move a distance equal to half their land speed on walls and ceilings during any given round. Double this allowed distance if taking a run action. The surface of any walls and ceilings moved along must be appropriate for running upon, if running, or for charging upon, if charging, aside from their vertical or upside-down nature, such that a ninja assassin cannot run along a wall that is strewn with obstacles, for instance. The ninja assassin need not move in a straight line the entire time when using Run On Walls, even if charging or running, but rather they can make up to two turns, each no more than 90 degree, during any such movement. Besides those two turns, however, they must move in straight lines, regardless of what sort of movement actions they are taking.
If the ninja assassin does not end their movement on a surface that they could normally stand on, they are subject to gravity as normal and may fall, though they can attempt one free action to grab hold of something, if they want to try hanging from that position, and only if there is something to grab. Attempting such is a Reflex save against DC 20, and creatures cannot be grabbed in this manner unless willing to try keeping the ninja from falling. Run On Walls only functions if the ninja assassin is wearing light or no armor, and carrying no more than a light load. Also, each use of Run On Walls requires a DC 20 Balance skill check beforehand, and a failed check means they cannot use Run On Walls that round.
Paired Weapon Mastery: At 10th-level, the ninja assassin perfects his special fighting style. He gains the benefits of the Greater Two-Weapon Fighting feat with any weapons mentioned in the Paired Weapons description. If he already possesses the feat, he instead gains a further +1 on weapon attack rolls and damage during any full-attack action where he attacks with only those weapons. The damage bonus is multiplied normally if a critical hit is scored. Paired Weapon Mastery only applies in light armor or no armor.