Alright, time to give the Soul Eater main protagonists their due.

Spoiler: Maka Albarn, Meister of Death
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Maka Albarn, Meister of Death
"Bring it on! I may be weaker than you, but I'll take whatever you throw at me!!" - Maka Albarn

Spoiler: Obligatory Image of Character
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Basics
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LG Human Paladin 4/Mystic Fire Paladin 2/Fist of Raziel 9/Witch Slayer 5
32 point buy
Starting abilities: STR 16, DEX 10, CON 12, INT 14, WIS 10, CHA 15
Increase Charisma at levels 4, 8, 12, 16, and 20


Build
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Level Class Base Attack Bonus Fort Save Ref Save Will Save Skills Feats Class Features
1st Paladin 1 +1 +2 +0 +0 Concentration 4, Diplomacy 4, Heal 4, Knowledge (Religion) 4, Sense Motive 4 Power Attack, Dreadful Wrath Aura of Good, Detect Evil, Smite Evil 1/day
2nd Paladin 2 +2 +3 +0 +0 Concentration 5, Diplomacy 5, Heal 5, Knowledge (Religion) 5, Sense Motive 5 - Divine Grace, Lay on Hands
3rd Paladin 3 +3 +3 +1 +1 Concentration 6, Diplomacy 6, Heal 6, Knowledge (Religion) 6, Sense Motive 6 Improved Sunder Aura of Courage, Divine Health
4th Paladin 4 +4 +4 +1 +1 Concentration 7, Diplomacy 7, Heal 7, Knowledge (Religion) 7, Sense Motive 7 - Turn Undead, Spellcasting
5th Mystic Fire Knight Paladin 5 +5 +4 +1 +1 Concentration 8, Diplomacy 8, Heal 8, Knowledge (Religion) 8, Sense Motive 8 - Smite Evil 2/day, Divine Spirit
6th Mystic Fire Knight Paladin 6 +6/+1 +5 +2 +2 Concentration 9, Diplomacy 9, Heal 9, Knowledge (Religion) 9, Sense Motive 9 Servant of the Heavens Spellshatter
7th Fist of Raziel 1 +7/+2 +7 +2 +2 Concentration 10, Diplomacy 10, Heal 10, Knowledge (Religion) 9,
Knowledge (The Planes) 1, Sense Motive 10
- Magic Circle, Smite Evil 3/day (Good-aligned)
8th Fist of Raziel 2 +8/+3 +8 +2 +2 Concentration 10, Diplomacy 11, Heal 11, Knowledge (Religion) 10,
Knowledge (The Planes) 2, Sense Motive 11
- Paladin Spellcasting +1
9th Fist of Raziel 3 +9/+4 +8 +3 +3 Concentration 11, Diplomacy 12, Heal 12, Knowledge (Religion) 11,
Knowledge (The Planes) 3, Sense Motive 11
Divine Might Smite Evil 4/day (Confirming), Paladin Spellcasting +1
10th Fist of Raziel 4 +10/+5 +9 +3 +3 Concentration 12, Diplomacy 12, Heal 13, Knowledge (Religion) 12,
Knowledge (The Planes) 4, Sense Motive 12
- Sanctify Martial Strike, Paladin Spellcasting +1
11th Fist of Raziel 5 +11/+6/+1 +9 +3 +3 Concentration 13, Diplomacy 13, Heal 13, Knowledge (Religion) 13,
Knowledge (The Planes) 5, Sense Motive 13
- Smite Evil 5/day (Holy), Paladin Spellcasting +1
12th Fist of Raziel 6 +12/+7/+2 +10 +4 +4 Concentration 14, Diplomacy 14, Heal 14, Knowledge (Religion) 13,
Knowledge (The Planes) 7, Sense Motive 13
Divine Armor Sunder Evil Item, Paladin Spellcasting +1
13th Fist of Raziel 7 +13/+8/+3 +10 +4 +4 Concentration 15, Diplomacy 14, Heal 15, Knowledge (Religion) 14,
Knowledge (The Planes) 8, Sense Motive 14
- Smite Evil 6/day (Fiendsmite), Paladin Spellcasting +1
14th Fist of Raziel 8 +14/+9/+4 +11 +4 +4 Concentration 15, Diplomacy 15, Heal 16, Knowledge (Religion) 15,
Knowledge (The Planes) 9, Sense Motive 15
- Paladin Spellcasting +1
15th Fist of Raziel 9 +15/+10/+5 +11 +5 +5 Concentration 16, Diplomacy 16, Heal 16, Knowledge (Religion) 16,
Knowledge (The Planes) 10, Sense Motive 16
Divine Vigor Smite Evil 7/day (chain), Paladin Spellcasting +1
16th Witch Slayer 1 +16/+11/+6/+1 +13 +5 +7 Concentration 17, Diplomacy 17, Heal 17, Knowledge (Religion) 17,
Knowledge (The Planes) 12, Sense Motive 17
- Smite Spirit Sharer
17th Witch Slayer 2 +17/+12/+7/+2 +14 +5 +8 Concentration 18, Diplomacy 18, Heal 18, Knowledge (Religion) 18,
Knowledge (The Planes) 14, Sense Motive 18
- Mettle
18th Witch Slayer 3 +18/+13/+8/+3 +14 +6 +8 Concentration 19, Diplomacy 19, Heal 19, Knowledge (Religion) 19,
Knowledge (The Planes) 16, Sense Motive 19
Sacred Vitality Locate Possession
19th Witch Slayer 4 +19/+14/+9/+4 +15 +6 +9 Concentration 20, Diplomacy 20, Heal 20, Knowledge (Religion) 20,
Knowledge (The Planes) 18, Sense Motive 20
- Slippery Mind
20th Witch Slayer 5 +20/+15/+10/+5 +15 +6 +9 Concentration 21, Diplomacy 21, Heal 21, Knowledge (Religion) 21,
Knowledge (The Planes) 20, Sense Motive 21
- Momentary Disjunction

Spoiler: Spells
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Spells per Day
Level 0lvl 1st 2nd 3rd 4th
1st - - - -
2nd - - - -
3rd - - - -
4th 0 - - -
5th 0 - - -
6th 1 - - -
7th 1 - - -
8th 1 - - -
9th 1 0 - -
10th 1 0 - -
11th 1 1 - -
12th 1 1 0 -
13th 1 1 1 -
14th 1 1 1 -
15th 2 1 1 0
16th 2 1 1 0
17th 2 1 1 0
18th 2 1 1 0
19th 2 1 1 0
20th 2 1 1 0


Maka's D&D 3.5 Treatment
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Maka's the main force behind her and Soul, as is the case with Meisters. As such, she needs to be a strong combatant, which is why she got the full BAB. Why Paladin? 1. She fights evil for a Lawful Good cause and acts like a Paladin. 2. Smite Evil. This is the basis of the Witch Hunt line of finishers from the anime (See Teamwork section below). Maka doesn't cast spells at all, so the average Wisdom score doesn't necessarily hurt her, and it can be bolstered with items. And the Divine Armor feat allows her to replicate the Black Blood if she needs it, even though that's more powered through Soul. Maka's Magic Circle also replicates her Grigori Soul and her Detect Evil and eventually Locate Possession and a Ring of True Seeing allow her to replicate the Soul Possession.


Sources
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Soul Eater Manga and Anime: This is why we came here folks...
PHB: Paladin base class
DMG: Power Attack
PHB2: Divine Armor
Dungeonscape: Divine Spirit
Champions of Valor: Mystic Fire Knight Paladin Level Substitution
Complete Warrior: Divine Might, Divine Vigor
Libris Mortis: Sacred Vitality
Book of Exalted Deeds: Servant of the Heavens, Fist of Raziel
Tome of Magic: Witch Slayer


Spoiler: Soul "Eater" Evans, Death Scythe
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Soul "Eater" Evans, Death Scythe
"Back away! I won't let you touch my Meister!!" - Soul "Eater" Evans

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Basics
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LG Human Evil Outsider Human Paragon 1/Marshal 2/Fiend of Possession 6/Marshal 11
32 Point Buy
Starting Abilities: STR 14, DEX 10, CON 15, INT 12, WIS 10, CHA 16
Increase Charisma at Levels 4, 8, 12, 16, 20


Build
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Level Class Base Attack Bonus Fort Save Ref Save Will Save Skills Feats Class Features
1st Human Paragon 1 +0 +0 +0 +2 Diplomacy 4, Hide 4, Intimidate 4, Knowledge (Arcana) 4, Listen 4, Perform (Piano) 4 Otherworldly, Dreadful Wrath Adaptive Learning (Perform (Piano))
2nd Marshal 1 +0 +2 +0 +4 Diplomacy 5, Hide 5, Intimidate 5, Knowledge (Arcana) 5, Listen 5, Perform (Piano) 5 - Skill Focus (Diplomacy), Minor Aura
3rd Marshal 2 +1 +3 +0 +5 Diplomacy 6, Hide 6, Intimidate 6, Knowledge (Arcana) 6, Listen 6, Perform (Piano) 6 Improved Initiative Major Aura
4th Fiend of Possession 1 +1 +5 +2 +7 Diplomacy 6, Hide 7, Intimidate 7, Knowledge (Arcana) 7, Listen 6, Perform (Piano) 7 - Ethereal Form, Hide Presence, Possess Object
5th Fiend of Possession 2 +2 +6 +3 +8 Diplomacy 6, Hide 8, Intimidate 8, Knowledge (Arcana) 7, Listen 7, Perform (Piano) 8 - Curse, Magic Item
6th Fiend of Possession 3 +2 +6 +3 +8 Diplomacy 7, Hide 9, Intimidate 9, Knowledge (Arcana) 7, Listen 7, Perform (Piano) 9 Draconic Aura Control Object
7th Fiend of Possession 4 +3 +7 +4 +9 Diplomacy 7, Hide 10, Intimidate 9, Knowledge (Arcana) 8, Listen 8, Perform (Piano) 10 - Animate Object, Possess Creature
8th Fiend of Possession 5 +2 +7 +4 +9 Diplomacy 8, Hide 11, Intimidate 10, Knowledge (Arcana) 8, Listen 8, Perform (Piano) 11 - Ally or Enemy, Possess Noncontinuous Object
9th Fiend of Possession 6 +3 +8 +5 +10 Diplomacy 9, Hide 12, Intimidate 11, Knowledge (Arcana) 8, Listen 8, Perform (Piano) 12 Imperious Command Control Creature
10th Marshal 3 +4 +8 +6 +10 Diplomacy 10, Hide 13, Intimidate 12, Knowledge (Arcana) 9, Listen 9, Perform (Piano) 13 - -
11th Marshal 4 +5 +9 +6 +11 Diplomacy 12, Hide 13, Intimidate 13, Knowledge (Arcana) 10, Listen 10, Perform (Piano) 14 - Grant Move Action 1/day
12th Marshal 5 +5 +9 +6 +11 Diplomacy 13, Hide 13, Intimidate 13, Knowledge (Arcana) 12, Listen 12, Perform (Piano) 15 Skill Focus (Intimidate) -
13th Marshal 6 +6/+1 +10 +7 +12 Diplomacy 14, Hide 14, Intimidate 14, Knowledge (Arcana) 13, Listen 13, Perform (Piano) 16 - -
14th Marshal 7 +7/+2 +10 +7 +12 Diplomacy 15, Hide 15, Intimidate 15, Knowledge (Arcana) 14, Listen 14, Perform (Piano) 17 - Major Aura +2
15th Marshal 8 +8/+3 +11 +7 +13 Diplomacy 16, Hide 16, Intimidate 16, Knowledge (Arcana) 16, Listen 15, Perform (Piano) 17 Double Draconic Aura Grant Move Action 2/day
16th Marshal 9 +8/+3 +11 +8 +13 Diplomacy 17, Hide 17, Intimidate 17, Knowledge (Arcana) 17, Listen 17, Perform (Piano) 17 - -
17th Marshal 10 +9/+4 +12 +8 +14 Diplomacy 18, Hide 18, Intimidate 18, Knowledge (Arcana) 18, Listen 18, Perform (Piano) 18 - -
18th Marshal 11 +10/+5 +12 +8 +14 Diplomacy 19, Hide 19, Intimidate 19, Knowledge (Arcana) 19, Listen 19, Perform (Piano) 19 Improved Toughness -
19th Marshal 12 +11/+6/+1 +13 +9 +15 Diplomacy 20, Hide 20, Intimidate 20, Knowledge (Arcana) 20, Listen 20, Perform (Piano) 20 - Grant Move Action 3/day
20th Marshal 13 +11/+6/+1 +13 +9 +15 Diplomacy 21, Hide 21, Intimidate 21, Knowledge (Arcana) 21, Listen 21, Perform (Piano) 21 - -

Auras Known:
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Auras Known
Level Minor Auras Major Auras
1st - -
2nd 1 0
3rd 1 1
4th 1 1
5th 1 1
6th 1 1
7th 1 1
8th 1 1
9th 1 1
10th 2 1
11th 2 1
12th 3 2
13th 3 2
14th 4 2
15th 4 2
16th 5 3
17th 5 3
18th 5 3
19th 6 3
20th 6 3


Soul's 3.5 Treatment
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Soul is in truth, more of a support character, being a focus for Maka's abilities and enhancing both her and her allies abilities and performance. As such, it came down to me choosing Bard or Marshal for this role. Bard felt right for Soul, however, his music doesn't translate well while in weapon form, as he has no hands to use music with. So it turned into Marshal, which fits a little better with what the Auras can do for the party. At low levels, Soul uses a custom item of Rary's Telepathic Bond to communicate with Maka in battle and buff her, and as soon as he can, he replaces that with a Helm of Telepathy, allowing him to use his Auras (which require being heard) across all allies. This is following the idea that since Soul becomes Ethereal when possessing the weapon, he takes his equipment with him, allowing him to use things like the Helm of Telepathy. This build also reflects Soul's growth as a character, starting out as a human Paragon with intent to perform like his brother, and then he found out he's a Demon Weapon, and he begins studying to become a Weapon, culminating in his 4th level, the start of Fiend of Possession. As he and Maka work together, they both grow, and Soul becomes able to bolster Maka's abilities with his Auras.


Sources
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Soul Eater Manga and Anime: This is why we came here folks...
PHB: Improved Toughness, Skill Focus, Improved Initiative
UA: Human Paragon
Player's Guide to Faerun: Otherworldly, Dreadful Wrath
Miniatures Handbook: Marshal
Dragon Magic: Dragonic Aura, Double Dragonic Aura
Drow of the Underdark: Imperious Command


Spoiler: Teamwork
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Maka and Soul as a Team
Maka and Soul can work individually as I've built them, but together, they are a force to be reckoned with. Maka fights primarily for the duo while Soul supports her by in the first round, using his Aura to buff their initiative score and then buff her damage on a Charge when its their turn.
Demon Weapon Form
Maka and Soul do have one advantage of Soul's abilities and their chosen form of Combat: They share a weapon. This allows them to upgrade it more easily by pooling their money for this purpose, making it a bit easier to get their hands on something like a +6 Holy Greater Dispelling Sudden Stunning Keen Adamantine Scythe. Even then, when Soul gets to level 10, he can add up to a +6 bonus to their weapon, allowing it to hit harder, or he can add new enchantments depending on the situation, like Flying to replicate that manga scenario where Maka rides Soul like a Witch on a broomstick, Defending to add to Maka's AC (which would be impressive already with appropriate armor), or Valorious and Holy Burst to add to Maka's Smite Evil+Power Attack.
Witch Hunt/Majin Hunt/Kishin Hunt
Maka and Soul's Signature Technique through Soul Resonance. Maka can do this on her own with Smite Evil+Power Attack, but early on, Soul adds in the Holy Enchantment or the Valorious Enchantment to buff that damage. As the pair progress, they can improve their shared weapon, allowing Soul to play around with other useful Enchantments without having to spend money on them. At their best, Kishin Hunt allows them to Smite Evil against someone with I'd say a -4 to Attack, then that adds a +8 to their attack damage, as well as the Charisma bonus from Smite Evil, a second or more Charisma Bonus from Divine Might, an extra point of damage to Evil creatures (1d4 to evil outsiders and evil undead), and then Valorous from Soul DOUBLES the damage done. There's plenty of other add-ons that can come in here (Such as the class features from Fist of Raziel), but I'll stop there.


Alright, I think that's everything!