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If you aren't at 100% but have done everything there is to do, you may of missed a special mission or didn't defeat an AC in one of the missions. Listed below is all known AC's that are in missions and extended missions.

Information provided by: NineballAlpha

AC's in Missions

1st Layer: District 2

• Defend the Arena: Gaidoz can be killed to his dismay in order to get the most money from kills. His death doesn't count for or against you. It's just plain fun.
• Secure Trene City: Red Eye can become an enemy if you attack her.

1st Layer: Special Research

• Defend Ruglen Laboratory: A prototype AC is attacking a fellow AC. You must move fast to save him.
• Disable Radar Bases: If you complete this mission fast enough by just destroying the dishes you will be asked to accept another mission where you must fight Backbreaker and Flare.

1st Layer: Nature Area

• Defend Water Processors: AC Megalo attacks after the first wave.

2nd Layer: Waste Disposal

• Disarm Bombs: AC Stratsbourg attacks while you're disarming the first bomb. He's a hover AC so he can stand to be on the molten waste.
• Disable Pulse Generators: An unidentified AC attacks you when you've disarmed half of the pulse generators in the lower section of the air ducts.

3rd Layer: District One

• Eliminate Intruders: AC Crossback.
• Protect Alloy Sample: AC Grinder attempts to take the sample after you cross the two big doors.
• Destroy the AC: AC Chain Impact is the object in this obviously titled mission. You get a bonus for destroying the flunkies along the way.

3rd Layer: Industrial Research

• Defend Personnel Convoy: If you complete this one well enough, (i.e. don't let the convoy get destroyed) you get to fight AC Chain Impact in the bonus mission.
• Destroy Kisaragi Forces: AC Claizen and shows up after you defeat the rest of the mine. Your partner Street Enemy helps you out if you really need it.

4th Layer: Energy Production

• Defend Energy Reactor: If you complete the gauntlet of energy shields, gun turrets, and a huge energy blast coming at you, you get to fight an unidentified quad AC in the reactor room.
• Investigate Magna Ruins: After you take out the camouflage MT's in the ruins, AC Fanfare turns out to kill you. Your paired partner AC Huntress joins him.
• Infiltrate Rehito Lab: AC Nocturne attacks after you are done with the computer core.

Layered Hub

• Infiltrate Layered Hub: Two prototype AC's come out and play before you face The Controller core.

Dual Missions

1st Layer: Special Research

• Disable Radar Equipment: Move fast to destroy just the radar dishes and you will be asked to fight AC's Backbreaker and Flare if you accept.
• Destroy Gun Emplacements: Don't bother with the hidden MT's shooting at you. Just target the immobile targets that shoot grenade rounds at you. Then you will be asked to accept the Distract Union Defenses Mission.

1st Layer: Nature Area

• Defend Water Processors: If you do well on this mission, in other words, don't let too much damage come to your targets, you'll be asked to Eliminate the Bombers. Just shoot the transport if you want to decline.
• Protect Capsules: This is just like capture the flag. You have too flags if neither of them are captured you get to Defend Helicopter Crew.

3rd Layer: Industrial Research

• Defend Personnel Convoy: Don't let a lot of your targets get destroyed and you'll be asked to face AC Chain Impact in Destroy the AC.