Mother

Mother is a boss added in The Binding of Isaac: Repentance, acting as the only boss of Corpse II, as well as the final boss of Ending 21. She is an undead version of Mom.

Behavior

Upon entering the boss room in Corpse II, the player will find nothing inside but a hole in its center. Walking into it will make the player character drop down into the arena where Mother is fought.

First phase

Mother begins the fight attached to the top of the room and does not move from there, similar to Mega Satan. Her attacks are:

One of Mother's hands grabs a knife and throws it down the side of the arena. The knife emits projectiles while travelling and upon impacting the back wall.
One of Mother's arms releases trails of projectiles that move across the arena in a waving pattern, eventually homing in on Isaac.
Mother throws a large Fistula ball at Isaac that bounces off the walls and releases projectiles. Mother will hit this ball back at Isaac several times before it bursts, sending projectiles in all directions.
Mother summons a horde of Dead Isaac's at the bottom of the arena that walk up towards Mother. These can be killed, but any that reach Mother will be hit towards Isaac.
One of Mother's hands shoots trails of projectiles across the arena and summons three Small Maggots.

Second phase

After losing enough health, Mother retracts her head and arms into her body before releasing a large green laser down the middle of the arena. She then separates from the top wall, expanding the arena and beginning the second phase. From this point on, she begins using completely different attacks:

Mother spins around in place, shooting out strings of projectiles in all directions.
Mother inhales and draws Isaac to her as projectiles appear behind Isaac. After that, she will shoot a massive ball of projectiles that split multiple times on hitting a wall or Mother.
Mother leaves the arena before charging vertically across one half of the room, then across the other. The half she charges across first is telegraphed by a splat at the top or bottom of the room. After this, she slams down in the middle of the room, sending rock waves and projectiles in all directions.
Faint lines appear either horizontally or vertically across the arena before Mother quickly shoots projectiles along the lines. This attack is repeated several times.

Damage Scaling

Damage scaling is an unclear mechanic introduced by Nicalis in The Binding of Isaac: Afterbirth to provide a more challenging experience to the players, enabling some enemies to retaliate against high damage attacks by deploying an "armor" of a sort to greatly reduce the amount of damage taken. Further details and an in-depth explanation may be found here.

Notes

Chaos Card works on Mother but will only kill one of her phases.
Using Plan C will kill Isaac before Mother as her death animation is longer than 3 seconds.
Rotten Tomato can cause Mother's wavy projectiles during the first phase to target herself.
The ball of splitting projectiles in Mother's second phase can also collide with Mother. The player can therefore move to the opposite side of Mother after she fires to to more easily dodge the attack.
The back wall of the fight is actually part of Mother's model; attempting to summon her via the console will change the wall of the current floor to a Corpse wall.
Unlike most other bosses, Mother has no health bar in either of her phases, so it is impossible to tell how much damage you are dealing to her without Spider Mod.

Gallery

Mother in-game.
Mother in her second phase.

Unlockable Achievements

A Strange Door - Defeat Mother.

Jacob and Esau - Defeat Mother.

Isaac's Awakening - Defeat Mother.

Meat Cleaver - Defeat Mother as Isaac.

Yuck Heart - Defeat Mother as Magdalene.

Guppy's Eye - Defeat Mother as Cain.

Akeldama - Defeat Mother as Judas.

Eternal D6 - Defeat Mother as ???.

Bird Cage - Defeat Mother as Eve.

Bloody Gust - Defeat Mother as Samson.

Devil's Crown - Defeat Mother as Azazel.

Tinytoma - Defeat Mother as Lazarus.

'M - Defeat Mother as Eden.

Lost Soul - Defeat Mother as The Lost.

Blood Puppy - Defeat Mother as Lilith.

Keeper's Sack - Defeat Mother as Keeper.

Lil Portal - Defeat Mother as Apollyon.

Bone Spurs - Defeat Mother as The Forgotten.

Revelation - Defeat Mother as Bethany.

Magic Skin - Defeat Mother as Jacob and Esau.

Dice Bag - Defeat Mother as Tainted Isaac.

Mother's Kiss - Defeat Mother as Tainted Magdalene.

Lucky Sack - Defeat Mother as Tainted Cain.

Number Magnet - Defeat Mother as Tainted Judas.

Ring Cap - Defeat Mother as Tainted ???.

Lil Clot - Defeat Mother as Tainted Eve.

Swallowed M80 - Defeat Mother as Tainted Samson.

Azazel's Stump - Defeat Mother as Tainted Azazel.

Torn Card - Defeat Mother as Tainted Lazarus.

Modeling Clay - Defeat Mother as Tainted Eden.

Crystal Key - Defeat Mother as Tainted Lost.

Adoption Papers - Defeat Mother as Tainted Lilith.

Cursed Penny - Defeat Mother as Tainted Keeper.

Apollyon's Best Friend - Defeat Mother as Tainted Apollyon.

Hollow Heart - Defeat Mother as Tainted Forgotten.

Beth's Essence - Defeat Mother as Tainted Bethany.

Found Soul - Defeat Mother as Tainted Jacob.

Godhead - Earn all 5 / 9 (except Ultra Greed) / 10 / 12 Completion Marks on Hard mode as The Lost.

Trivia

As revealed in the Ending that comes after this fight, Mother and Mom are the same person, with Mother being a representation of Mom from Isaac’s perspective.
- With this in mind, Mother could be considered a posthumous version of Mom.
She was formerly called "The Witness" in the Antibirth mod.
- The Witness itself was first designed as a boss mockup by the name of "Ur-Gurdy", tying it into the Mama Gurdy line and explaining its visual similarities to that line.
Between her original appearance in Antibirth and Repentance, Mother’s boss fight was changed drastically, including the arena being shrunken dramatically, the replacement of several attacks with new ones, the boss theme being changed, and the boss’s death animation being changed, along with the addition of Mom’s voice lines during the battle.
Mother's boss theme is called "Morticide", which is a play on words on both "Mortis" (meaning dead) and the root word "cide", meaning to kill. It can likely be inferred that "Morticide" means killing the dead.
Unlike Mom and Mom's Heart, Mother is not instantly killed by using The Bible.