All bosses from Sonic 3 & Knuckles including minibosses and the secret final boss. I also did both Sonic and Knuckles' story bosses. A lot of people don't realize that the different stories actually do have some major differences. Also, holy wow this video ended up longer than i anticipated.

Timestamps:

Sonic's Story:

Fire Breath (Miniboss) 0:03
Dr. Robotnik (Angel Island Zone) 0:18
Big Shaker (Miniboss) 0:52
Dr. Robotnik (Hydrocity Zone) 1:25
Tunnelbot (Miniboss) 2:04
Dr. Robotnik (Marble Garden Zone) 2:20
Bowling Spin (Miniboss) 3:03
Dr. Robotnik (Carnival Night Zone) 3:33
Big Icedus (Miniboss) 5:12
Dr. Robotnik (IceCap Zone) 5:48
Twin Hammer (Miniboss) 6:12
Dr. Robotnik (Launch Base Zone) 6:42
Dr. Robotnik (Launch Base Zone) 7:06
Hei Hou (Miniboss) 7:37
Dr. Robotnik (Mushroom Hill Zone) 7:54
Gapsule (Miniboss) 8:35
Barrier Eggman (Miniboss) 9:05
Dr. Robotnik (Flying Battery Zone) 9:50
Guardian (Miniboss) 10:35
Dr. Robotnik (Sandopolis Zone) 11:34
Heat Arms (Miniboss) 12:25
Dr. Robotnik (Lava Reef Zone) 13:14
Knuckles the Echidna 14:40
Mecha Sonic 15:58
Mecha Sonic 16:16
Mecha Sonic 16:49
Red Eye (Miniboss) 17:37
Death Ball (Miniboss) 19:11
Kyodai Eggman Robo 20:10
The Doomsday Zone 22:07

Knuckles' Story

Fire Breath (Miniboss) 24:47
Eggrobo (Angel Island Zone) 25:06
Big Shaker (Miniboss) 25:30
Eggrobo (Hydrocity Zone) 26:12
Tunnelbot (Miniboss) 27:17
Eggrobo (Marble Garden Zone) 27:53
Bowling Spin (Miniboss) 28:39
Big Icedus (Miniboss) 29:04
Eggrobo (IceCap Zone) 29:32
Twin Hammer x2 (Miniboss) 30:05
Eggrobo (Launch Base Zone) 30:58
Hei Hou (Miniboss) 33:01
Eggrobo (Mushroom Hill Zone) 33:21
Gapsule (Miniboss) 34:01
Barrier Eggrobo (Miniboss) 34:33
Dr. Robotnik (Flying Battery Zone) 35:18
Guardian (Miniboss) 36:09
Eggrobo (Sandopolis Zone) 37:14
Heat Arms (Miniboss) 37:59
Mecha Sonic 38:45