I'm trying to figure out which secret achievements count towards the Top Secret achievement. Progression achievements like those that unlock the Classic Firestar team-up seem not to count towards this.
With the help of @TheOrangeBird I was able to determine that secret achievements do not count towards the percentages for each category, so doing math to figure out what you're missing won't help find them. The missing achievements that count towards percentages are all progression achievements like the ever increasing amount of kills needed in different game modes or the Burning Crusade one for Classic Firestar. So unfortunately that means we're going to have to stumble across them by accident.
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FOUND SECRET ACHIEVEMENTS OR MYSTERY OBJECTIVES - CLICK BELOW TO SEE THE ANSWERS
Mystic Mystery, Volume 2 - As Colossus with Magik as your active team-up defeat Limbo bosses and a bunch of Mayhem demons in MM or Infernal Limbo. Also defeat Mister Sinister with any hero/team-up combo. I did it with Cable/Firestar personally. - Events > Mystic Mayhem - Counts as 1 towards Top Secret.
Mystic Mystery, Volume 3 - Doesn't seem like a specific team-up is needed for this one. Defeat Loki 3 times as Loki in Story Mode (or ICP?). Defeat Juggernaut 3 times as Juggernaut in Terminals on any difficulty. Defeat Taskmaster 3 times as Taskmaster in Terminals on any difficulty. Other clone matchups may work too, but this one is confirmed twice. Doom vs. Doombot wave in MM counts as well. NOTE: CURRENTLY THIS STEP ISN'T COUNTING TOWARDS TOP SECRET. THIS IS PROBABLY A BUG THAT WILL BE FIXED WITH A FUTURE PATCH.
Whispering Winds - (Part 1 of Pirate Deadpool Team-Up Chain) Anywhere in Buccaneer Beach with any character that has the listen emote type /listen 10 times into the chat box. This achievement is the first in a chain to unlock the Pirate Deadpool team-up and does not count towards Top Secret until the chain is complete. - Miscellaneous > Advanced - Does not count towards Top Secret.
Message In A Bottle - (Part 2 of Pirate Deadpool Team-Up Chain) As far as I could tell you just get this after killing a certain amount of enemies on Buccaneer Beach. The enemy that dropped it for me was not elite. This achievement gives you the message in a bottle item with clues to 5 parts of a treasure map - Miscellaneous > Advanced - Does not count towards Top Secret.
Pirate's Treasure Map, Fragment 1 - (Part 3 of Pirate Deadpool Team-Up Chain) This can drop from a Ninja elite in a number of zones. So far Hidden Cove, Bamboo Forest, ICP and MM have all been reported. - Miscellaneous > Advanced - Does not count towards Top Secret.
Pirate's Treasure Map, Fragment 2 - (Part 4 of Pirate Deadpool Team-Up Chain) This can drop from a Junkyard Thug elite in Hood's Cargo Freighter. Can be done in Story Mode or Terminals. - Does not count towards Top Secret.
Pirate's Treasure Map, Fragment 3 - (Part 5 of Pirate Deadpool Team-Up Chain) This can drop from Dark Elves elites in the northern part of Norway, near the Ancient Ruin Site waypoint. Can also be down in MM and Kurse terminals. - Does not count towards Top Secret.
Pirate's Treasure Map, Fragment 4 - (Part 6 of Pirate Deadpool Team-Up Chain) This can drop from Moloids in the Wakanda one-shot. People have also reported having it drop from a Jabari Tribesman in the Wakanda one-shot. - Does not count towards Top Secret.
Buried Treasure - (Final Part of Pirate Deadpool Team-Up Chain) This can drop in any public area in Chapter 7. This is the final step and counts towards the Top Secret achievement. Counts as 1 towards Top Secret.
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Never Gonna Give You Up - Defeat Taskmaster 1000 times in Cosmic Terminals - Miscellaneous > Advanced. Counts as 1 towards Top Secret.
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My Own Wurst Enemy - Defeat Kurse in Greed, Red and Cosmic Terminals while equipped with Fred Dawson's Hot Dog Cart - Enemies > Adversaries - Counts as 1 towards Top Secret.
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Oh, Canada - Equip Guardian's Battle Suit unique on Wolverine and perform the Cheer emote using /Cheer in the chat box. - Heroes > Wolverine - Counts as 1 towards Top Secret.
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Independence Day - Equip Iron Patriot Repulsors unique on Captain America and perform the Salute emote using /Salute in the chat box. - Heroes > Captain America - Counts as 1 towards Top Secret.
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NOTE: THERE'S A SECRET ACHIEVEMENT FOR DEFEATING BATROC 1000 TIMES, BUT IT'S NOT ON THE LIST YET BECAUSE I DON'T KNOW THE NAME OF THE ACHIEVEMENT. I'LL ADD IT ONCE I GET MORE INFO.