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The following is a list of the secret objectives that are in each of the chapters
Chapter 1 - Mission 1:
Involve Loki in the fight. (Go next to her with both characters and interact)
Chapter 1 - Mission 2:
Kill ALL enemies
Chapter 1 - Mission 3:
Destroy ALL the Mytrans attacking the cities
Chapter 1 - Mission 4:
Capture the temple before the end of round 10
Chapter 1 - Mission 5:
Find the secret technology on a small remote island. (northwest of the map)
Chapter 1 - Mission 6:
Unlock the secret mission. (Move a unit to a strange-looking item at the new part of the map)
Chapter 1 - Mission 6s:
Get the secret technology hidden at one of the cells.(in the middle of the northwestern-most cell)
Chapter 1 - Mission 7:
Hover over the chasm with one unit. (before the exit point)
Chapter 2 - Mission 10:
Get full immunity against the insect. (located southwest of the map)
Chapter 2 - Mission 11:
Don't let anyone die in your army
Chapter 2 - Mission 12:
Occupy both temples
Chapter 2 - Mission 13:
Defeat Jama without killing other enemy units
Chapter 2 - Mission 14:
Defeat a human unit with the turrets
Chapter 2 - Mission 8:
Capture the armory and the research center to gather information
Chapter 2 - Mission 9:
Do not let Nunzio Escape
Chapter 2 - Mission 9s:
Capture every building in the human base
Chapter 3 - Mission 15:
Neutralize the defense system. (Destroy the 2 power plants)
Chapter 3 - Mission 16:
Save at least one person from the group facing the Kondor forces. (save the Buggies next to the first two
Enemy Destroyers after crossing bridge)
Chapter 3 - Mission 16s:
Find Bakunin's lost supplies. (in the middle area, and return to him)
Chapter 3 - Mission 17:
Defeat Agni without any casualties
Chapter 3 - Mission 18:
Meet the mysterious Jon Remedy (at the end of the southeast path, near the prang)
Chapter 3 - Mission 19:
Use the secret exit to leave. (After freeing the scientist, the secret exit is located at the west, interact to open)
Chapter 3 - Mission 20:
Finish the mission in 25 turns
Chapter 3 - Mission 21:
Destroy the radar unit (Intruder seen after defeating first batch of enemies - kill the scout)
Chapter 4 - Mission 22:
Don't kill any humans when using Eli or Rachel
Chapter 4 - Mission 23:
Protect ALL allied units. (aka Don't let anyone die?)
Chapter 4 - Mission 24:
Capture ALL radar stations
Chapter 4 - Mission 25:
Get access to the engine room. (enter small room under Loki for Green Card)
Chapter 4 - Mission 25s:
Finish the mission without killing a hostile unit
Chapter 4 - Mission 26:
Destroy only two of the door controllers