- Charging a non-dimming Sword chip will cause MegaMan to warp 2 steps forward before executing the chip attack at double damage.
- Reflect: Pushing B + ← will put up a shield. If a non-Breaking attack hits the shield, the attack is negated and 50 damage is dealt to the nearest enemy down the row. Other Navicust programs that use B + ← will be overridden.
- Charge Shot: WideSword (a regular WideSword that deals out 80 damage and in MMBN5, gains a 10 damage power boost for any additional levels to the Buster Power)
- Bosses to use against:
- Weakness: The Proto Soul does not allow Program Advances to be charged, but most of the P.A.'s don't need it anyways. Also, the StepSword can leave MegaMan open to a Slasher, and any direct contact while using StepSword on an enemy will leave MegaMan injured. Also, Like Guts Soul, Proto Soul is very limited in range when it comes to the charge attack.
- Proto Soul tends to be used only by players who have mastered its Sword boost ability. This especially applies to those who have mastered the Variable Sword/Neo Variable input commands, which can cause especially high damage in a singe chip.
- The MoonBlade series from BN5 also made Proto Soul more viable, since players can combine the Sword boost ability with these Battle Chips to execute the attack in the middle of the enemy area, making it nigh-impossible for the chip to miss.
MegaMan's Charge Shot becomes a Dark Sword attack, hitting a 3 x 2 space for 400 damage in a fashion similar to the Life Sword Program Advance. With a single AreaGrab, the attack is capable of covering the entire enemy area, making it impossible to miss.
MegaMan gains this soul during the battle with ShadeMan.EXE. As they are being pummeled by him, ProtoMan gives him the Soul to help him survive the battle as ProtoMan is too badly weakened by the Dark Chip to help. He uses this form to defeat Dr. Regal while he is Cross Fused.
MegaMan NT Warrior MangaMegaMan first uses Double Soul with ProtoMan. After Serenade is absorbed by Bass, MegaMan and ProtoMan fiercely fights Bass. Despite heavily injured and at disadvantage against the Dark Navi, Bass feels that their auras becoming stronger. Realizing that MegaMan and ProtoMan's unity is executing the program left behind by Serenade, Bass gathers large amount of dark powers to kill both of them, refusing to accept power of bonds and such. MegaMan and ProtoMan charges straight at Bass and feels their soul resonating, performing Double Soul strong enough to cut through Bass' attack. MegaMan Proto Soul immediately turns the tide, heavily injuring Bass. Accidently, he punched down Bass to right in front of ProtoMan's defenseless body. However, Bass chose not to delete ProtoMan, choosing to defeat MegaMan with his own effort. Both Bass and MegaMan unleash their last attacks, with MegaMan emerges victorious.
MegaMan once again uses Proto Soul during his final battle against MegaMan DS. ProtoMan offers his power to MegaMan, just as MegaMan DS attacks them to prevent them using Double Soul, but they succeeded and MegaMan Proto Soul continuously attacks MegaMan DS, fatally injuring him. However, MegaMan DS absorbs LaserMan to gain more power. MegaMan attacks him again, but cannot destroy the Dark Aura protecting MegaMan DS. After encouraged by Bass, MegaMan attacks again with SearchMan's assisstance by shooting Hyper Magnum to destroy the Dark Aura. The Dark Aura cracked from the shot and MegaMan uses the last bit of Proto Soul's power to destroy the damaged Dark Aura. The last attack was not enough to destroy the barrier, but MegaMan able to destroy it by punching it through and defeat MegaMan DS with Giga Cannon.
- In Battle Network 4's Blue Moon version, MegaMan is able to use Soul Unison with the DarkSword Battle Chip that appears during the second ShadeMan fight, provided he is not in a worried state. This is due to the Dark Chip appearing for story mode purposes.