The Captain Vaga quest line is its own game mode and the EXP scales with your level. It's an area you transform in, so don't worry about your HP or damage. The kill count is what determines how much EXP you gain, so the higher the number, the more EXP you get. You will also gain something called Promotion Points. Promotion Points are what increases your rank. The amount you get is calculated by multiplying your kill count by 2. Failure to complete a mission can happen if either you or an outpost loses all HP. If you managed to kill something, you are only rewarded with EXP. Sometimes during missions, the client will fail to load your score. So when this happens, go into Task Manager to close the game, load the game back up, log in, and it should fix itself to give you your well-earned EXP. Normally you can enter into a mission 20 times a day, but if you visit the Mess Hall, you can purchase Warm Soup for 600 credits to allow extra missions to be taken after reaching the daily limit for 10 minutes. The only other worth-while thing to purchase from the Mess Hall is Sweet Candy, and it also costs 600 credits. It grants 10% additional EXP for 10 minutes (grants at the mission result screen).
After reaching the final rank of Elite, you will receive the Captain Vaga Medal and the stats on it are +8 ALL, +800 HP/MP, and +6 W.ATK/M.ATK. You will also be able to purchase a chair that heals 200 HP/MP from the CS89 machine in the Mess Hall for 5000 credits. This chair, by the way, is awesome! When you sit with it, it can play either the In-Battle music, the Captain Vaga Official Soundtrack, or a heartfelt musical piece .

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Controls:

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Your character must be equipped with a weapon outside of Captain Vaga in order for damage to register. There are some other equips that you may also benefit from like having a poison effect (quite effective against the boss) on your weapon or having armour that has HP regen (this will likely be the thing that will carry you).
You move your character with the WASD keys and aim with the mouse (W = up, A = left, S = down, D = right).
Switch between your main weapon and pistol with 1 and 2.
Tapping A twice dashes you to the left and tapping D dashes to the right. When either falling or Bunny Hopping, you can dash in the air up to two times before landing.
R is the key you reload your main and secondary weapons with.
The left mouse button is used for firing/piercing.
The right mouse button (while held in conjunction with firing/chopping with the left mouse button) is used to focus a large amount of shots in one burst and to empower your melee attacks.
Spacebar: tap once to "Bunny Hop", tap twice to Jag Jump. S + Jump = Jump downward.
C is used to access your Tactical Support menu. You can use upwards of 4 at a time and be used with 1, 2, 3, and 4 when the menu is open.
Aiming up while in the midst of using a Tactical Support skill gives you easy access to receive the ammo/summon you desire, as it will be deployed to your location.
EFG are designated as your Special Equipment. You can have upwards of 3 at a time.

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Ranks

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Guardsman employs the use of the Submachine Gun, Quantum Spear, Grenade, Ammo, Repositioning Boost, and Swift Assault.
Second Guardsman employs the use of the Rifle, First Aid, Healing Generator, Squad Shield, and Tactical Mastery.
First Guardsman employs the use of the Shotgun, Auto Turret, Short Range Marksmanship, and Vital Strike.
Lead Guardsman employs the use of Adrenaline Shot, Orbital Bombardment, and Quartermaster.
Enforcer employs the use of Level 2 Suits, Minigun, Overwhelming Firepower, and Stamina Boost.
Third Enforcer employs the use of Booster Shot and Cloak.
Second Striker employs the use of Level 3 Suits.
First Striker: able to upgrade Quantum Spear to level 4. Unlocks Personal Office.
Lead Striker: able to upgrade Quantum Spear to the max level of 5.
Elite is the final rank. The rank of Captain.

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Primary Weapon

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Submachine Gun (Maxed out at Level 3)- Ammo: 60. Magazines: 4. Base Damage: 5. Max Damage: 7.
Rifle (Maxed out at Level 3)- Ammo: 40. Magazines: 4. Base Damage: 10. Max Damage: 12.
Shotgun (Maxed out at Level 3)- Ammo: 24. Magazines: 6. Base Damage: 5. Max Damage: 7.
Launcher (Maxed out at Level 3)- Ammo: 30. Magazines: 3. Base Damage: 300. Max Damage: 360.
Flamethrower (Maxed out at Level 3)- Ammo: 500. Magazines: 1. Base Damage: 30. Max Damage: 32.
Quantum Spear (Maxed out at Level 5)- Base Damage: 20 (Empowered: 40). Max Damage: 28 (Empowered 56).

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Secondary Weapon

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Pistol (Maxed out at Level 3)- Ammo: 13. Magazines: 4. Base Damage: 5. Max Damage: 7.

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Special Equipment (All MAX out at Level 3)

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Frag Grenade: tosses a grenade in whatever direction you’re aiming and detonates in 3 seconds, so predict accordingly where your enemy will be. Base Damage: 30. Max Damage 36.
First Aid: Using it will instantly heal you. Base Heal: 10. Max Heal: 30.
Adrenaline Shot: Increases Speed by 30% for 30 seconds.
Booster Shot: Increases stability of shots fired and also increases your melee damage. Base Damage: 10. Max Damage: 20.
Calming Shot: Provides increased stability.
Jump Pack: A mega jump that propels you forward in the direction you're moving (not to be confused with where you're aiming).

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Tactical Support (All MAX out at Level 3)

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Ammo: Request additional ammo (may takes upwards of 6 seconds to deploy).
Healing Generator: Continuously restores HP to allies within range (may takes upwards of 6 seconds to deploy).
Squad Shield: Creates a shield on the map that takes damage before your HP. Cooldown activates when the shield breaks (may takes upwards of 6 seconds to deploy).
Auto Turret: A turret that emits shockwaves to damage and pull nearby enemies (may take upwards of 6 seconds to deploy). Base Damage: 3. Max Damage: 5.
Minigun: A heavy weapon with high rate of fire and penetrating shots (may take upwards of 10 seconds to deploy). Ammo: 350. Base Damage: 10. Max Damage: 12.
Orbital Bombardment: Fire a series of powerful blasts from orbit to devastate enemies that are ground-level (may take upwards of 10 seconds to deploy). Tip: try to keep flying bugs close to the ground because damage will not register if they're too high in the air.

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Tactical Doctrine (All MAX out at Level 3)

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Repositioning Boost: Increases Speed after aiming.
Short-Range Marksmanship: Increases reload speed.
Overwhelming Firepower: Increases the default number of magazines. Base Increase: 4. Max Increase: 6.
Swift Assault: Increases attacks per second.
Vital Strike: Increases melee damage. Base Damage: 10. Max Damage: 20.
Stamina Boost: Increases max HP. Base HP: 110. Max HP: 120.
Tactical Mastery: Reduces Tactical Support cooldown.
Quartermaster: Reduces Special Equipment cooldown.
Cloak: Increases Defense.

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The Gist of this Game Mode:

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Before you head out to battle, stop by the Mess Hall by pressing W on the door. You will be brought to an open area that has stairs leading to a platform. Go up there and use the portal to navigate to the third area. It looks the same as the floor before, but trust me, you did change floors. Just head on through the door to the left and you will enter the Mess Hall. When you enter the room, talk to Mess Officer. He will give you fetch quests to collect 10 bug samples in exchange for 100 Credits. There are 5 fetch quests in total. I suggest getting a total of 20 samples because you will need 10 more samples for a fetch quest you get later on at Second Striker. After receiving the quest, head back to the transporter and go to the floor that says Bridge. Go through the left door and you will be back in the room you started in.

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Your starting rank is Guardsman. As such, your first mission is to defend an outpost by killing bugs with either a gun or a spear.

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I've found that the Rifle and Quantum Spear work the best for the first two bugs because they're capable of one-shotting them. You gain additional skills later on and can be upgraded with credits that you earn after every successful mission to be used in 2 areas on the Strategic Support & Logistics Management floor. In Passageway 2 through the left door, you can upgrade your weapons. Again, in Passageway 2, there is a hidden door to the right side of the map through the center of what I've dubbed the "black-void"; inside you can upgrade your Tactical Support. I've found that it is pointless to upgrade any weapon and the distribution instead should be focused as follows: First Aid, Quantum Spear, Booster Shot, Orbital Bombardment, Grenade, Minigun, Auto Turret, Short Range Marksmanship, Tactical Mastery, Quartermaster, and then Cloak.

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When you reach the rank of Enforcer, you will make your way down into the bug's main base (the one that you saved Lapis from) and this time your top mission is to race to locate and eliminate all bug eggs. Luckily they're all in one spot so when you enter inside the base the first time, just head south-west to find the eggs.

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Once you get to First Enforcer, look out for the next time you enter a mission. A new character by the name of Miro joins the story and he's annoying. He's rigged the next outpost defense mission lowering the amount of ammo you get from Ammo Deploy and I'm about to tell you how to get around it. Grab Rifle, Ranged Suit 2, First Aid, Minigun, Orbital Bombardment, and Quartermaster. Once deployed, instantly summon up your Minigun and high tail it to the far left side of the map and aggro all the bugs to you. Some will try to attack the outpost, but get rid of them and return to the spot you were luring. Rinse and repeat until you have a hoard of bugs following you around and just stall out the clock. When the timer reaches less than 20 seconds, let loose on them with that Minigun and predicted Orbital Bombardment!

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Having gotten your spear to Level 3, your empowered attacks will deal 48 damage. Combine that with the Level 3 Booster Shot and now your empowered damage is 68. Level 3 First Aid restores 30 HP. Level 3 Grenade deals 36 damage. Level 3 Orbital Bombardment deals 400 x 4. Level 3 Minigun deals 12 damage. Level 3 Auto Turret deals 7 damage. Level 3 Cloak lowers damage. Needless to say, this is gonna be a lot more useful against the bug boss.
Once you've reached the rank of Striker, you'll be immediately forced to fight the bug boss. No other missions will be available until you have beaten it. Go into the mission with Level 3 Melee Suit, Quantum Spear, Grenade, First Aid, Booster Shot, Orbital Bombardment, Auto Turret, and Cloak. Clear out the map of the regular bug mobs and then head over to the far right of the map. Once you're there, try entering the portal. This will activate the appearance of the bug boss on the far left of the map. Rush over there and wait for it to poke its head out. Summon the Auto Turret to prevent it from moving anywhere. You're given 3 chances to summon Auto Turret and Orbital Bombardment while the boss moves across the map. For whatever reason while you're keeping pace with the boss and you use Auto Turret in lower path at the middle of the map, the boss gets confused and physically turns around heading in the opposite direction of its set course. This effect doesn't last long, since it does correct its designation. Stay in front of it and don't worry about getting knocked around by it. Cloak with Level 3 Melee Suit lowers the boss’s damage to 1. Pop the Booster Shot and take whichever one of your hands that is the best at mashing and go ham on the left mouse button while your other is holding the right button down. Use Grenade and Orbital Bombardment to help with additional damage. This is the ONLY method I've found that works.

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Now having disposed of the boss, you are given free reign to eliminate the hoards of bugs that appear on that map. Defeating the boss is still what completes the mission, but do you really want to? You just went through hell trying to kill it. Give your nerves a break and just enjoy the 10 minutes of bug genocide. From here on out, your only means of getting promotion points the safe way is by doing the egg destruction mission.

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Once you reach Second Striker, Miro will have you going on five fetch quests to gather 10 bug samples from Bug Soldier, Flying Bug Soldier, Advanced Bug Soldier, Advanced Flying Bug Soldier, and both Red Bugs. You must complete all sample missions before being able to continue getting promotion points. On an unrelated note, you can probably fight the bug boss a bit more easily now that you can upgrade the Quantum Spear to Level 4. Get as many kills as you can before summoning the boss through the portal on the left side (the boss appears from the right side this time). You use the same build as before, but this time you've got a stronger weapon.

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When you reach First Striker, you will be given your own office. You can go to it through Passageway 3 through the right door. Once you enter the room, you will enter a large empty room where you will be greeted by your own secretary who says she will help you with anything you need. Talking to her gives you instant access to the Logistics Management, Strategic Support, Mess Hall, Battle Preparation, and Office Customization. Immediately you will think, "how does customizing your office have anything to do with progressing in this game mode?" I'm not gonna lie, it does absolutely nothing for you than to simply make your office look like it's got "activity" going on in it. There's furnature you can purchase for 600 creidts each. You cannot interact with any of the furnature.

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When you reach the rank of Elite, you will be able to enter the Captain's Office and that is through the door to the right in Passageway 1. Congratulations! You've completed Capatain Vaga!