Wizard Lord (Lightning Scar, Medium) - The amazing Wizard Lord must feed on your most expensive towers every other round. If there are no towers on screen, the mission is over. Pass 30 custom waves of upgraded bloons.
Mix 'n Match (Ocean Road, Medium) - Get 1 free new tower every second round. Pass 50 extra hard rounds with reduced cash rewards and spending ability. Can you master the use of all towers in a single game?
The Crucible (Bloonhenge, Medium - Use the two "Sockets of Power" to grant super enhancements to the towers you put in them. Pass 25 brutally tough rounds using all your skill and cunning.
Money Management (Military Base, Apopalypse) - Amass a bank balance of $50,000 during the game to win. This will not be easy since the Bloons will come at you non stop and towers are limited to tier 3 or less.
Direct Assault (Custom Map, Medium) - The Bloons are attempting to overrun your position with brute force. Start with a handful of towers, you are limited to only Mortar, Dartling, Sniper and Spike Factories.
No Escape(Custom Map, Medium) - In this fiendish mission, the path has no exit. Survive 13 grueling rounds as the Bloons whiz around until they are popped. You have 30 seconds to destroy them, or you will lose a life every second after that.
On the Mobile and Steam versions, if you close out the game after the completion screen shows up for any Special Mission, you can keep playing in freeplay mode. This can add playability by allowing you to play with special rules, like tower limitations, tower lifespans, and the Wizard Lord tower consumption. You can also play fully on the unique tracks Protect Monkey Town and No Escape, however you're forced to play on Medium difficulty.
Completing a Special Mission first time will give a message saying that the player is a "chock full of awesomeness". This links with Ninja Kiwi's slogan "More awesomer".
If the player finished the Full House and MOAB Madness missions before March 8, 2012, they didn't get achievements for these missions. However, the missions can be replayed to get the achievements.