When you get to Ft. Eagle, the Professor will say that he thinks that the cell must be in the research facility.
You'll start in a forest where little bunnies are hopping around. An Army guy is wandering around looking for something that he dropped.
Meet Sebastian Apt
Farther along, you meet Sebastian Apt and his dog Hunt. The Army took Apt's memories. The professor says that it seems like the government has a secret agenda. Apt invites you to his house.
Terry follows automatically. The professor detects an SOS from a young girl who is now hiding in a cabin. Apt asks if the girl is about Apt's age and dressed like a pirate, but when he learns that the girl is younger, Apt says that she might have come from the Facility.
Apt will follow you. If you ever get separated from Apt or Hunt, you can just go back to the campfire where you met them, and talk to Apt. You might need to push the dog to make him move away from the campfire.
Make your way into the forest. The path winds around some trees and goes north. In the screen with the sheep, go to the left to find a guy selling stuff. He has potions, elixirs, bottles, and the recipe for potions. You might want to get a bunch of bottles so you can get lots of water from wells for making potions. Beyond the salesman there is an enemy snake and a treasure chest. The treasure chest has a butterfly knife inside.
There are some evil sheep up above. There is also a treasure chest with an elixir inside.
Go west from the evil sheep. Continue west to reach a screen with a treasure chest that contains a mallet. You can keep going west and you'll get to a screen where a fisherman is trying to catch a huge fish. There's nothing that you can do here yet, though, so go back the way you came and head south.
When you're near a couple of snakes at the bottom of the screen, go to the right to find a treasure chest with the Fancy Soup recipe inside.
Fight the Army
Get ready for battle. You should have at least two or three potions with you. You will also want to have all of your Trick Decals, so be sure to go back to the professor to restock the decals if you don't have all of them.
Then go south and Apt will walk toward his cabin. A bunch of soliders will appear, led by a red soldier. They tell you to cooperate and keep silent. When they say that there has been a restructuring, Apt asks if they got rid of Brad, who stole all of Apt's research. The red soldier says that they have obtained Element 117, which the professor says is what his power cells are made of. The Army found a galactic stone and got help from four others. They are going to destroy Apt's cabin to expand the Facility.
Press R or the green thing in the top-right to get to the Trick Decal screen. Make sure all of the brown soldiers are on screen, and use the Trick Decal with the question mark on it. It will turn the brown soldiers into farm animals. Then use the Mochi decal. After that, fight whichever soldiers are still there until they are all dead.
Meet Dolly
The red soldier will leave, and Apt will talk to you. You'll automatically go into the cabin, where you will learn that the girl, Dolly, was cloned, and her parents went home with the clone instead of her. Apt takes you aside and talks about how bad it is that the facility is doing forbidden research on humans. The professor says that it brings back memories. Seems like a strange thing to say... Anyway, he tells you to hurry to the facility because they've modified the power cells, which is very dangerous.
After Apt is done talking, you can read the newspaper clipping on his desk, which is part 2 of the CosmoNOTs special. It says that the CosmoNOTs protest the use of cells of element 117, which they consider to be dangerous. They claim to be pacifists, but they take radical action for what they believe in. They moved underground.
You can sleep in Apt's bed to save the game, or cook using his stove.
In the area south of Apt's cabin, you will find a treasure chest to the left with a large coin inside. There are soldiers around this area.
Army Knife Guy
In the southeast, there is a treasure chest that requires a key to open. If you don't have a key, you can get one soon, so be sure to return to this chest later when you get a key.
Inside is an Army Knife. This is the thing that the army guy dropped. He's near the professor's ship. Go back to him with the army knife and give it to him. You can get another army knife later. He will give you the Ja Dagna. This is the only opportunity to get the Ja Dagna, and the army guy will disappear after you defeat the boss here, so be sure to get the Ja Dagna!
Back to the Game
Go northeast, fighting soldiers on the way. You'll reach an area where a soldier is guarding a fence. Don't bother with him. You can't get through the fence that way anyway. Go around southeast, where some mobile missile launchers will attack you.
When you get past the launchers, you will find a vending machine. It contains some really useful stuff. Weapons, keys, food, etc. Some of it is a bit pricey, but worth it. Be sure to go back to the vending machine with more money later if you can't afford the stuff that you need. At the very least, you ought to buy some keys. They can unlock various treasure chests, as well as being able to open some doors.
Remember, if you get a key, go back and open up the locked treasure chest and give the army knife to the army guy (see the section above.)
When you're ready to move on, just push the vending machine out of the way. It's hiding a hole in the (not very secure) security fence. Go through the hole and open the chest to the left to get a Keycard.
Then, go back toward the right, but go past the facility entrance. You will overhear a soldier talking about an airport in the back. Go kill him, then go northeast to reach the airport.
Wolf Squadron
An Air Force soldier will say they blew their whole budget on building the airport, so they have no planes. When the guy is done talking, go down and kill all of them. If you want to use trick decals on them, you have to walk up to them to trigger a dialog where they say "Enemy Approaching." Three of the soldiers will turn into animals, but the leader will still attack. He has a pretty nasty green air-swirl attack that hits you a few times before disappearing, so keep an eye on your HP. Otherwise just keep attacking the guy until he dies.
The leader will then admit defeat, turn you into the Wolf Leader, and give you the Flyboy costume. It gives you air-based magic abilities.
The Facility
Now you can head into the facility. First, get past the blue soldier who is going around the loop. He's easy to avoid if you don't want to fight. Then take the lower fork. You will find a treasure chest with a Potion inside.
In the next room, there are a couple of soldiers going back and forth in a loop. Past them, there is a blue soldier, and a treasure chest past him that contains Steak.
Go south from there, then to the right, up a ramp, toward another blue soldier. Past him, you can go south into a room. There is a chest in here that contains an Elemental Staff, and there are some little grey men floating around. You can fight them or just ignore them.
Continue through the previous room, which has a straightforward path to the next room. There are a couple of soldiers at the base of some stairs. At the top of the stairs is a red soldier. Beyond the red soldier are some mobile missile launchers.
In the next room, you'll see a single blue soldier, then when you go north there are a couple of brown soldiers who might run away from you, depending on your level, as well as a red soldier. The door at the upper-right has a bed and bath inside. There is also a computer that you can check on to read about the Mu Control System (MCS,) which uses Element 117 to digitally control living creatures. It is considered a biological weapon that is outlawed on all R3 planets.
When you exit this room and go to the left, you will find a locked door in the back wall. Use the Keycard on the panel to open the door. You will find a Saber and Tonfa in the chests (as long as you have keys to unlock them,) but you can't unlock the middle chest yet.
Now go back out, and go to the west. After you continue along the path, a scientist will appear. You find out that a clone, known as "Snake," is on the loose. Then a bunch of scientists rush past.
Fight Snake
In the next room, there's a scientist who didn't manage to escape. The doors become locked, and then Snake attacks. It's just a big black snake with red spots. Its attacks are just like the snakes that you encountered before, but this one has more HP.
When it's gone, go to the left side of the room and open the chest to get an Elixir (if you didn't already.) Then I recommend that you go back the way you came and go to the room with the bed and bath so you can heal up and save the game.
Go back through the room where you fought snake. You will encounter some black-and-green monsters. They are pretty easy to avoid if you go around them. When you get back up on the green ledge on the other side of the black-and-green monster area, go south to get a ?-Decal from a treasure chest. Then go up through the door.
There are more black-and-green monsters, and a red soldier. Past them, you find a treasure chest that contains Blue Eyes v 2.
In the next area, there will be a floating silver cube enemy past the door. You can just go through the door; there's nothing past it but that cube. In the next room, you will pass by three floating cubes.
Lester Sprawl, Round 2
Then, in the next room, you will encounter none other than Lester Sprawl. He admits that he and his fellow CosmoNOTs are pursuing the Professor, trying to get the Element 117 of his power cells. Lester says that the professor stole the cells from the CosmoNOTs. The professor says that the CosmoNOTs stole the cells from him first, and the professor was simply taking back his rightful property.
Lester says that the professor is from a different planet, and says that it's bad of the professor to use Terry like this. Lester says that Mint, who is Terry's age, is designing their plasma engine. The only thing that they're missing is cells. The professor realizes that Mint has discovered how to convert cells into plasma for the engine, or perhaps for some dangerous weapons. The professor urges Terry to stop Lester and Mint.
Lester says that Mint is not only skilled with machines, but is also the youngest CosmoNOT and a popular singer.
Then he'll attack. Use the Cloud Sword against Lester, since it's stronger against humans. You can also try using the Mochi sticker against him. And if you have Tech Points, use them to do stronger attacks. Otherwise, just keep your HP up and keep on hitting Lester.
When he's done, he'll talk to Mint, saying that they're restoring power to the cells. He asks if she wants to input the code now. She'll soon be starting up a weapon, so Lester tells Terry that he'll have to hurry to stop her.
You can go ahead and go back to the bath and bed room to heal and save. After you pass through the room where you fought Lester, you will be in a room with two silver cubes. Go to the left and up through the door. Go up the hallway and you meet Mint. She claims that the cells originally belonged to the CosmoNOTs. The cells in the machine passed the final test, so she doesn't need to fight Terry. But she promises that the CosmoNOTs will take back all the cells so they can convert Element 117. Then she runs north. Go north.
The Machine
The battle against the machine works like this: some soldiers will materialize in the area. When they are there, the machine at the top of the screen is invulnerable, so you have to kill the soldiers before you can attack the machine.
When fighting the soldiers, stay at the bottom part of the screen, where it's easier to finish off the soldiers without them ganging up on you. When they are gone, don't press B! You will already get put out of battle mode when the soldiers are all gone, so it will slow you down if you press B after the soldiers are gone.
With the soldiers gone, run up and attack the glowing machine in the top center. Use Techs on it to deal more damage.
Sometimes a symbol will show up on the bottom-right of the screen, like a sword, boot, or heart. These symbols will disrupt your fighting, making it take longer to defeat the soldiers. But you can get rid of that symbol by tapping the big minus sign in the top-right of the area. It changes the channel that is being displayed on the monitors, turning off the symbol in the corner. If the minus sign doesn't work, try the plus sign.
Repeat the pattern of killing the soldiers, running up and attacking the machine, and pressing the minus or pluss button to change the channel, until you have destroyed the machine.
When the machine is destroyed, the power cell will fall from above. Use a Cell Decal to capture it. Then you can use the ship decal to get back to the ship. There are still enemies in the base.
Go in and talk to the professor. He'll say that the government was likely involved with Area 52. But he realizes that Mint ran off with something, and says it could cause trouble later.
The professor adds Aegis to the SeaNavi. The professor adds a Trick Decal called the Constellation Decal. It fully heals your HP. Of course, you can only use it once, and then you have to return to the professor to get another, so use it carefully.
When you're ready, set the SeaNavi to Aegis.