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You can upgrade your ship with the upgrade box that randomly appears when you destroy an enemy. This upgrade box floats on your screen until you either pick it up or the level ends. By shooting the box its icon will cycle to the next upgrade. When the upgrade reaches the last icon, it will cycle to the first upgrade again and repeat. If you don't shoot the upgrade box, it will cycle to the next weapon after about 5 seconds. You can use this box to your advantage as you play. Once you acquire the upgrades, they will remain on your ship until your ship is destroyed, (or if you are able to press square and eject it). Your upgrades are as follows.
The shield has one level. It provides a blue force field around your ship that will allow you to take one hit and survive. After you take that hit your ship will flash and be invincible for just a few seconds (which should be enough to get you away from heavy fire). the shield will NOT protect you if you plow into a boss, and your ship will obliterate with or without the shield if you crash into them. The shield is a very important component to your ship and is reccomended to be your next upgrade if you don't have any shield.
Rear Gun 1/1
The rear gun has one level. When you pick up this upgrade it will allow your ship to shoot one stream behind your ship. This is a good thing to have, but not as important as the others. However it is extremely helpful when enemies come up behind you, or if you need to avoid fire and destroy an escaping enemy.
Spread Gun 1/1
The spread gun has one level. When you pick up this upgrade, it will allow your ship to shoot 3 streams in a wide spread in front of your ship. This not only increases your damage, but can help to clear a wider path than the default single line gun can provide.
The missiles have 2 levels. When you pick up the first level of this upgrade, it will launch two missiles from the back of your ship on either side. The missiles launch and fall back and away from the ship, then they accelerate past the ship and curve into the front of the ship (but do not cross each other). When holding down the level 1 missiles will come out every 3 seconds. But witl level 2 missiles they will come out every 1.5 seconds, providing more damage. While the missiles are slow, they are extremely powerful, and a direct hit with just one missile will do significant damage to both enemies and boses. A missile will have no effect on the the upgrade boxes, they will not detonate on them, they will not change them, and will only pass through them.
The laser has one level. The laser takes place of your forward gun, which means when you pick it up, you will no longer have the default gun. If you have the spread gun, the middle shot will be replaced with the laser, while the left and right gun will still be the standard shot. Regardless of whether you pick up another spread shot, the laser will remain as your forward gun until your ship is destroyed. With the laser equipped, when you hold the fire button the laser will shoot one long burst about 3-4 seconds long, however it will be out of service for about 3 seconds. The laser can also be fired quickly by pressing x, which is an optimal way of using it, as it will always be charged and capable of inflicting much more damage. Lasers also have no effect on the upgrade boxes, and will not change them as the standard gun will.
There are five levels for the options. Options are the little pods that float around your ship by default, or which can follow you (toggled by R1), or which can be paused in their current place (holding R1). The beginning options shoot about one standard shot per second. For the first 3 levels of options, you will acquire a pod for each upgrade, to a maximum of 3 pods (level 3). After you have received the 4th level, the pods will double their shot speed, which will be about 1/2 your standard shot speed. When you have picked up the 5th option, the 3 pods will shoot as fast as you, and will be quite powerful, and deadly.
You can upgrade your ship in any way you please, however keep in mind that when you are using 6-7 upgrades it is often hard to find further upgrades. I've noticed that there can be streches of up to 3 full levels before the next upgrades appears. Because of this, it would be wise to upgrade your ship fully first. Begin with shields, pick up your spread gun, get missiles, equip the laser, and then the back gun. After this you'll want to get the last level of missiles and then focus on upgrading the 5 levels of options. Generally you should be able to get through the first 2 levels without options, so in the early levels they are not important, but they do become extremely helpful from the 3rd level and onward.
One final note, your shield should be your top priority. If you lose your shield at any time, be sure to make that your next upgrade, as you'll never know when the next upgrade will be after that one. If you are in dire need of a shield with no upgrades in sight, you can often times press square and eject the last upgrade you received, which will send the upgrade floating around the screen. then you only need to wait for it to turn back to shield before picking it up again.