This is a breakdown of the Special Missions and their objectives. I've debated personally what Missions should be included in the Level Leaderboard or not, as not all of these Missions have significant objectives. If you have anything to add regarding this, feel free to post below!

Time Attack Missions: Ghost Babel was doing speedruns before it was cool, but these are exactly the same as doing the Regular Stage. None of these are included on the leaderboard.

Stage 1 Mission 1 Stage 4 Mission 1 Stage 6 Mission 1 Stage 7 Mission 1 Stage 8 Mission 1 Stage 10 Mission 1 Stage 12 Mission 1

Distance Based Missions: A variant on the Time Attack, each step Snake takes is about a meter. Stage 3 Mission 1, Stage 5 Mission 1, and Stage 11 Mission 1 require you to finish the missions within 2500 M. Stage 12 Mission 2 requires a completion within 600 M. Currently the only Distance Mission I have included on the boards is Stage 12, as it adds challenge to the MG GANDER fight. Stage 5 and 11 may be worthwhile additions, but definitely not Stage 3. Even a rusty run of Stage 3 gave me ~1400 M.

No Alerts: As the title implies, you cannot be discovered!

Stage 2 Mission 1 Stage 4 Mission 2 Stage 6 Mission 2 Stage 9 Mission 1 Stage 11 Mission 2

No Damage: As the title implies, you cannot take damage!

Stage 3 Mission 3 Stage 5 Mission 2 Stage 7 Mission 2 Stage 13 Mission 1

Stages 7 and 13 are pointless, given that both are faster if you don’t take damage. Stages 3 and 5 make more sense as a challenge run.

Boss Challenges: Defeat a boss with x weapon. The Mission jumps straight to the boss fight, which is nice.

Stage 8 Mission 3 – Bison with Mines Stage 11 Mission 3 – Viper with Grenades Stage 12 Mission 3 – GANDER with C4 (just the legs) Stage 13 Mission 3 – Viper with Grenades

Bomb: If you stand still for more than a second, a bomb will explode and kill Snake. Mostly irrelevant for Any%, but interesting for Excellent rank.

Stage 4 Mission 3 Stage 10 Mission 2 Stage 13 Mission 2

Collect the FOX-HOUND Emblems: The obligatory collect-a-thon, there are 4 hidden emblems to find. The fourth patch will finish the mission.

Stage 1 Mission 2 Stage 3 Mission 2 Stage 8 Mission 2

…Everything else: Most of these oddball missions are included on the leaderboard. I’ll give a description of each mission.

Stage 1 Mission 3 – Start at the end of the stage and return to the beginning (go back to the HALO jump)

Stage 2 Mission 2 – Guards are constantly on Alert

Stage 2 Mission 3 – Meet Mei Ling, which you do by calling her frequency at various points across the map, then head to the exit

Stage 5 Mission 3 – You must travel through all of the box sorters. :(

Stage 6 Mission 3 – Destroy all the ghosts who are spooking the Stage. You can destroy them with a single punch. Don’t wear IR goggles to see them.

Stage 7 Mission 3 – You must survive the artillery strike for 60 seconds, which cannot be a speedrun. Thus none of Stage 7’s special missions appear on the board.

Stage 9 Mission 2 – Destroy the power plant by planting C4 in the following locations: B1: B-2, C-3, 1F: B-3, and 2F: C-4. There are cracks in the airducts marking these locations (apparently). These instructions are provided by Campbell.

Stage 9 Mission 3 – Put on your thermal goggles to find four spots (ducts) coming out of the walls, set the C4 at those points. These instructions are provided by Campbell.

Stage 10 Mission 3 – Climb up the hill with the broken artillery guns, and avoid barrels a la Donkey Kong. Fair warning, the barrels do great damage. Some barrels bounce and some roll down the hill.

Credit to Paul Keating’s Special Stage guide on GameFAQs for a lot of useful information https://www.gamefaqs.com/gbc/914401-metal-gear-solid/faqs/8361