After you beat the game, you will be allowed to try EX Mode. When you start, check you inventory to see a nice selection of weapons and armor. You will also be given access to the Chrysler Building. The building consists of 77 randomly generated levels complete with some very nasty monsters. If you get through all 77 levels, you can take on a very difficult Boss. If you beat him, you will be rewarded with an entirely new ending.
Chocobo Cameo:
After you've visited the museum the first time, go back to it on the map screen. As the helicopter view scrolls around the building, look at the banner.

Get 60 rounds of bullets:
On the first level, after you beat Eve on the Opera Stage, go backstage and you will see the hole. If you listen carefully at the hole you will hear sirens. Go back outside the Operahouse and ask the cop on the far right for bullets. He will give you 60 rounds.

Infinite Bullets:
In the NYPD go downstair and enter the left door. You can find the bullets in the box near the counter get it and go out to the New York map. Now return to that room for more bullets. Repeat as needed.

Infinite Life:
(submitted by: BestCheater)
Use all the medicine you have whenever you can, do that for a while and then it wont work anymore because your life cannot go down anymore, you are now invincible.

Infinite Medicine:
This trick is similar to the code for infinite bullets. In Day 3:Selection, after the battle in the NYPD #17th District where Torres will die and Wayne will take over for him, whenever you leave the precint and come back, visit the weapons room and check the chest to the top right. There will always be a medicine 2 or 3 waiting for you everytime.

Lots of Trading Cards:
When you're at the hospital, just before you go to the 13TH floor, find the room that has the nurse who is looking for more hurt people. Now go to the top of the room to the fallen cabinet, look behind it to find lots of tradng cards. Make sure you have room for them in your inventory.

Normal and Super Tool Kit:
When in the EX game, collect as many Rare Trading cards as possible. If you ask Wayne to show you his collection he'll give you tool kits at certain numbers. So, if you ask Wayne to show you his collection after you have given him 12 or so Rare Trading Cards, he'll give you a tool kit. It acts as an infinite amount of regular tools.

If you give Wayne 14 or more Rare Trading cards, and ask him to show you he'll give you the Super Tool Kit. This acts as an infinite amount of Super Tools.

The Real Ending:
After you win you'll be asked if you wish to save. Do so, then reinsert CD #1 and choose the EX game. You'll now see the Chrysler Building on the Manhattan map. Go inside and make your way to the top to see the real enemy and ending.

Tuning Up the Ultimate Gun
There are two Ultimate guns in Parasite Eve. The first one can be acquired when going through the regular game, while the other is only available in the EX mode. There are a few steps in getting this powerful weapon.

You must get the G3A3 "rifle", the M870 "shotgun", the PPK "Pistol", and the M9 rev2 or the M800 "pistols". The G3A3 can be found in the Hospital, the M870 can be found in the sewers of China Town, the PPK is found at the entrance of the warehouse, and the M8000 or M9rev2 are in the Museum.

Use your tools and select the G3A3 as the primary weapon.

Now select the shotgun and select the [Burst] option to put it on the rifle. Take the PPKs [first strike] option and put that on the rifle. Then take the [double command] from one of the two pistols. These options when combined can destroy Eve with little or no trouble. With the remaining tools take the +attacks from your other weapons and the +offense items and pump them into your new rifle.

Put your Bonus Points into the attack and you can have a rifle with over 125 attack when you fight the T-REX. Its a good idea to tune up armor so that it has an auto heal function.

Warning: Do not put any special abilities on the rifle like "fire, freeze, acid, etc..." because some enemies are very strong against certain atributes.

Also do not put any 2x, 3x, 5x, or any others because your weapon's damage is divided by the number of shots you have.

Later on you can get the FA-MAS from the Crystler building, which has a base attack of 119 and a base range of 169, but you'll have to get ride of the 3x with a supertool.

Ultimate Weapon:
If you give 300 pieces of junk to Wayne, he will build you a weapon of mass destruction. Choose the RIFLE. This is by my experience the best weapon in the game. It has an attack of 150+ and a range of 185.

Eventually you will want to add the following special abilities...

Command +2 or +3
Burst
First Strike
Critical Attack Up
Acid -- If it doesnt affect the creature the weapon will still do maximum damage.
Tranquilizer -- For the same reason as acid.
Cyanide -- For the same reason.

Weapons from Junk:
Have you ever wondered why you got so much junk in Parasite Eve Have you also wondered why Wayne always asked you to get rid of junk Well, if you give Wayne more than 300 pieces of junk, he can make AWESOME weapons from them. Just make sure that you TELL him what to make, instead of letting him decide because he screws up sometimes.

Alligator Attack:
When you enter the sewers you will have to fight a alligator he will use his tail and mouth. You will need to level up on walking around and finding rats to get in a battle with or else you'll pay for not leveling up.

Secret Weapon in Museum:
After you deactivate the alarm in museum, head right (by pressing D-pad Down-Right) and you will find a lift which can only go to 4th floor, and in this floor you will find a secret room with a few box in it

Navigating through the Chrysler building:
When looking for the item room, go right or left before going up or down. When looking for the stairs leading up to the next floor, go up whenever possible. After defeating a Boss on one of the "tenth" floors (10, 20, 30, 40, etc.), go to the elevator, go to the first floor and leave the building. Then, go to the police department and give any unneeded items to Wayne and save the game.

Tips for winning the game:
Complete the game as normal, then complete it in EX mode one or more times. Keep the same armor used when the game was completed the first time. Use all the extra bonus points to strengthen your weapon and armor, then go to the Chrysler building and use tools to strengthen new weapons. This is done by examining at the starting specs of the weapons. Example: An attack of 30+1, range of 20+2, and bullets of 40+0; refer to the first numbers. Use tools to move the parameters, and remember to do the same with your armor. Get all of the rare trading cards out of the Chrysler building and give them to Wayne to get the tool kit and super tool kit to upgrade your weapons as much as possible. Also remember to have a lot of room in the inventory for the final battle with Eve.

Tip for Ammo:
You wanna save ammo? No problem, just do this, when ever you put a weapon in storage or dispose it, go to use item icon and select the weapon, click reload, press the button until all the ammo in the gun is in the ammo box, then store it or dispose it.

Secret Area In First Sewer:
When you beat Eve in the Rehearse Room (THE ROOM WITH THE PIANO) and enter the sewers, fight the two battles, go to where the little girl is. When you see her she will run through the gate. Don't follow her! Go up until you reach the top of the screen, go all the way right, then hold right-down and walk, soon you will enter a small room with three ammo boxes.

Helpful Helper:
I have messed up once, and I don't want anyone to make the same mistake. When you beat the game remember this clue! The things that Wayne engrave your name on are the things you will get to have in EX mode. Please don't make the same MISTAKE! I know because I had a G3A3 that I named the Jackal the first time, when the second time came, it had a damage of 246............ I chose to name the P228, I lost the Jackal.

Gun tip:
If you have a good gun, don't put any 2x 3x or 5x, maybe even 7x or 10x on your gun because it divides your damage by whatever times you fire it.