Version 1.2 of the game added secret alternate phases to three boss fights, two of which being ideas that were originally scrapped before the game's release:
•Botanic Panic!: Spoiler:By not attacking Ollie Bulb the onion, he will retreat back into the ground and skip to Chauncey Chantenay the carrot's phase featuring an additional mini-boss, a spinning radish named Horace Radiche who despite being completed before the game was released, originally went unused.
•Pyramid Peril: Spoiler:If the player shrinks into the mini-plane form just before the fourth phase of the fight, Djimmi the Great will scan the player and pull up a marionette featuring a dinosaur, a miniature version of Dr. Kahl's Robot and a stone statue, before tugging a longer string and pulling up a smaller version of Cuppet. This skips the fourth phase and goes directly into a harder version of the final phase where the smaller Cuppet will act as a turret firing at the player counter-clockwise to the spinning Eye of Providence pyramids.
•Dramatic Fanfare: Spoiler:By parrying off of the pink star projectiles, the player can land onto two hanging cherub props that control the chandelier in the background of the first phase. Standing on one will gradually lower it until a dinging sound is heard and the chandelier becomes slanted. Doing the same to the other cherub will cause the first phase to abruptly end and trigger an alternate storyline to the fight that was originally unfinished by the time the game was released. After both cherubs are lowered, Sally Stageplay's newlywed husband is crushed by the chandelier. Instead of changing the scenery to Sally's home, the second phase of the fight takes place at St. Timothy's Nunnery, implying that Sally became a nun. In place of Sally's husband worrying in the bushes for her is the Priest that oversaw their marriage, and a Nun takes the place of Sally's children to throw rulers at the player. In the third phase, a god form of Sally's husband accompanies Sally's goddess form and attacks by summoning a cherub, portrayed by Sally's son from the normal second phase of the fight, to push a spinning cardboard fireball towards the player. The fourth phase of the fight is unchanged from the normal path, but with the Nun appearing in the background in place of Sally's husband and children when on Expert mode.

One boss fight in "The Delicious Last Course" DLC also features a secret phase:

•Doggone Dogfight: Spoiler:During the second phase with the circling jetpack puppies, their jetpacks will produce white exhaust fumes when they have plenty of health, with the more damage taken turning it into gray exhaust to indicate that they have low health. If all four jetpacks are spewing gray exhaust at the same time with none of them having been defeated, the Dog Chinook will appear and eat them before grabbing the plane as if it were the normal third phase. However, the puppies and the Chinook pilot will appear in portholes on its paw pads instead of the laser satellites, where they throw regular and pink Pineapple Mint grenades that explode into shrapnel when they are hit. The Chinook pilot also appears and calls for the vessel to shoot homing fire hydrant missiles.
Contributed by MehDeletingLater
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