Classic Mode - Allows you to play each of the games with exactly the same content and aspect ratio they used back in the day. Features a number of optional borders to use on widescreen monitors, and also a number of toggles such as screen size, pixel scaling accuracy, CRT filter options, dithering transparency filters, etc.
Anniversary Mode - Allows you to play each of the games in modern aspect ratios, as well as make use of a number of different toggle options such as what abilities Sonic has (Instashield, Drop-Dash, Spindash, etc.), CD and 3&K's OST's, which Sonic sprite to use, and whether or not the player has a limited pool of lives. Also features local/online co-op for Sonic and Tails or Knuckles and Tails. Features optional remastered OST's for Sonic 1 Genesis/Mega Drive, Sonic 2 Genesis/Megadrive, and Sonic 3&K.
Completion of Anniversary Mode as Sonic unlocks Metal Sonic as a playable character in Anniversary Mode. Completion of Anniversary Mode as Sonic, Tails, and Knuckles unlocks Amy as a playable character in Anniversary Mode. Alternatively, both characters can be unlocked easily via a cheat code.
Metal Sonic features an increased jump height, cannot spindash, but damages enemies with his Peelout. Amy cannot spindash or spin attack and does not curl into a ball when she jumps, but can attack enemies with her hammer, perform a high hammer jump, and hammer springs to gain extra height. She can also destroy destructible rocks and etc. with her hammer.
Story Mode - Select a character and play through Sonic 1-3&K as Sonic, 2-3&K as Tails, or Knuckles' Story in 3&K with new animated scenes building up on the characters unique perspectives on the events that transpired in the 4 main games. Also features toggle options such as lives on/off, CD and 3&K's OST's, which Sonic sprite to use, etc. Features optional remastered OST's.
Coins - Can be obtained when lives are disabled the same way lives and continues are obtained or through mission mode/boss attack. Can be spent in the Museum, to retry Special Stages in Anniversary/Story modes, etc. Can be spent instead of continues in Anniversary/Story if lives are enabled and you run out of continues.
Museum - Allows you to spend collected coins to unlock OST's, concept art, comic book covers, animations, dev interviews, etc. to view at your leisure. Can also purchase game sets of Special Stages to replay as much as you like, and new special stage layouts to play in.
Boss Attack - Comes in several modes, each with limited lives. Separate mode lets you choose a game to go up against it's gauntlet of boss battles. Combined mode pits you up against all of the bosses from all of the games in chronological order or in order of difficulty, Random mode pits you up against a series of random bosses, Endless Mode gives you 1 life to survive as long as you can against a never ending boss gauntlet.
Speedrun Mode - Allows you to speedrun through individual acts in the various games. Based on Anniversary Mode.
Online Leaderboards - Can be toggled between local, friends, and worldwide. Allows you to compare your scores/times from Boss Attack and Speedrun Mode with those of other players in your area, friends list, and across the whole planet. Also features a replay upload feature to show off that your scores are all legit and how you obtained them. You can browse through replay data, download the replay data of others to watch, etc. Everything is bragging rights on the leaderboards, you do not actually unlock anything for securing high scores.
Mission Mode - Allows you to complete a variety of optional missions to obtain coins. Some missions require other missions to be completed or other conditions to be met to unlock them. Completing all missions unlocks Metal Sonic as an optional sprite set for Sonic in Anniversary Mode.