Here are the 9 hidden objectives.

Blockhead - Mission 1 / Prevent the blockade from taking more than 25% damage.
Master Tactician - Mission 2 / Complete the operation by constructing fewer than 30 mobile units.
Not the Bees! - Mission 3 / Take out the enemy air defenses.
Pro Anti-Air - Mission 3 / Take out the prison's defensive structures.
Agent Provocateur - Mission 3 / Capture all of the Security Stations.
Experimental Fanatic - Mission 4 / Build at least eight Experimental units.
A Czar is Born - Mission 6 / Build your first Darkenoid.
Bot Lord - Mission 6 / Complete the operation with an army made up entirely of Assault Bots (you cannot build any other type of units).
Supremest Commander - Mission 6 / Prevent any enemy King Kriptors from crossing the main fortress bridge.