After completing the Forest Area and returning back to the Machine Village, your next objective will be to visit the Flooded City. You can reach the area by going through the section where the big crater in the middle of the City Ruins is located. There will be a large sewer pipe you can travel through that will take you directly to the place where the Flooded City is located.
Right before you enter the open area of the Flooded City, there is a Acces Point just outside of the large pipe you come from. Activate it as you travel into the area. You'll see a bunch of destroyed buildings submerged in ocean water as you enter the area. You can jump along the building platforms across the water to reach your objective. Along the way, you can actually fish in the open water towards the sea, doing so will allow you to obtain the Pod B in the water pointing towards the sunlight.
When you reach the area on the other side near the giant missile, you'll need to destroy all of the enemies nearby. Its a small group of enemies that shouldn't be difficult to defeat, doing so triggers a small dialogue that leads into the next section of the area. You'll board a flight unit that takes you to another air battle for your mission.
Fight your way through the waves of enemies that attack you during the next section. You can easily dispatch them with your ranged weapon or melee weapon as they attack you. As you progress through the level and defeat all enemies that appear, you'll eventually come face to face with another goliath class machine boss fight.
EditBoss Fight: Goliath Flyer
The Goliath Flyer is not a difficult boss to bring down. You'll have to continuously attack with your ranged weapon and avoid projectiles as you attack its central weak point. The flyer will continue to shoot projectiles at you that must be dodged or swiped away with your melee weapon. The large amount of projectiles shot at you may become annoying, but should not be hard to avoid.
As long as you continue attacking as you dodge, you'll bring the Goliath Flyer down easily. Once its defeated, the next section of the level will trigger as more enemies swarm on your position. A cutscene will trigger as the larger boss of the stage will appear from the water below. Though you won't be able to fight it just yet, you'll have to destroy all of the other enemies that appear on screen.
After a short time flying around and destroying smaller enemies, you'll find yourself faced with a large machine with yellow orbs. You'll have to destroy the smaller orbs that circle around the center in order to destroy the machine. While you are doing so, the machine will attack with both laser blast and projectiles that shoot from its center and smaller orbs. Avoid these attacks and take out each section of the machine to blow it up.
After another small flying section, a cutscene will trigger and you'll find 2B on the ground next to a large cannon. Walk up to the cannon to use it and fire a blast at the boss' open mouth. If you fire when it's mouth is closed, it won't deal any damage and begin charging up a counterattack. You need to stop it before it launches it's blast, otherwise you'll see one of the joke endings to the game and need to restart the level.
Hit the boss in the mouth twice to deal enough damage and trigger another cutscene. You'll once again take to the skies and fly around the boss, which has begun walking on two legs in the water.
EditBoss Battle: Ancient Machine Weapon
Destroy all of the smaller enemies that appear as you fly around the area. You'll fly right up to another machine with yellow orbs that you must destroy. Use the same strategy as before in order to move on. After flying around again, you'll find another machine with yellow orbs which you must also destroy. However this time you'll notice a countdown timer. If the timer runs out, you'll immediately fail the level and will have to restart everything all over again.
If you destroy both machines before the timer reaches zero, you'll see a cutscene that will signal the end of the stage. The next cutscene will directly lead into the the following objective.