There are six sets of weapons, each of which consists of a rapid fire weapon, a slower, but more powerful, heavy weapon, and a lock-on surface to air laser. At first only Weapon Sets A through C are available however, beating stages 5, 6, and 7 unlocks Sets D - F.
Generally speaking you want to use the rapid fire weapon against large numbers of weak enemies (so when you're not fighting a boss, basically) and the heavy weapon against bosses and strong enemies. There are a few exceptions in both cases, depending on the specific weapon and enemy.
Weapon Set A
The "balanced" set; none of these weapons have any major advantages over other sets, but they also lack a lot of their disadvantages as well. Both the rapid and heavy weapons are relatively powerful and fast, and the lock-on's ability to make tight turns make this a very practical set for a beginner that doesn't favor any particular style of attack.
- Machine gun: This a standard issue machine gun that is in every Contra game. It is offers a good balance between power and being able to sweep multiple targets. You can do a lot of damage quickly against one target, but you can not stand still and take everything out by spinning in circles like you can with other weapons
- Grenade Bomb: Launches a grenade, which bounces along the ground then explodes, doing good damage. If the grenade hits something it immediately explodes. It has a fairly good rate of fire and a medium range. The time-delay makes it excellent for taking out stationary target like snipers and cannons since you can run throw in a grenade when you have an opening and then run away.
- Lock on Missile: Four missiles fire outward and track the target very quickly. The missiles move directly at their targets, can rise rapidly, and are able to make tight turns. You are much less likely to have a missile hit a wall instead of the target with this set.
Weapon Set B
This weapons set offers a lot more power than the first set, however, each weapon has a few drawbacks, and it will take a bit of practice to become skilled enough to be able to handle them in battle.
- Fire Whip: The flamethrower from the last game returns, and is just as deadly at clearing out groups of enemies and stationary targets. It can also take out certain projectiles, so if you keep it going it acts as a small shield. Good for sweeping out small enemies and projectiles, but even better at stationary bosses since the damage adds up quickly.
- Charge Shot: Probably the hardest weapon to use, but the most powerful. Hold down the fire button to build up a charge (your weapon will glow red when fully charged) and release the button to fire. It is hard to use since it is slow and the projectile is very narrow, so you will miss often if you don't time your shots well.
- Lock on Laser: These lasers are similar in style as the lock on missiles. They are faster, able to make tighter turns, and you get five of them, however they are significantly weaker than any other lock-on weapon in the game.
Weapon Set C
This is more or less the "power set" of weapons. Both the rapid and heavy weapons are among the slowest but strongest of the original three. The spread gun is good against most groups of enemies, however there can be problems if you are being attacked on all sides. If you stand close to a single target, all of the spread bullets will hit, doing more damage than a fireball. The lock-on is very accurate but it's weakness will probably make you prefer a different Weapon Set.
- Spread Shot: A wave of bullets spread outward in a ~30 degree arc, so aiming is not a problem. Each shot does a fair amount of damage; enough to take out grunts, but not really good against artillery, vehicles, and bosses. There is also a significant amount of time between rounds fired, in fact some heavy weapons are faster.
- Classic Fireball: The standard fireball that has been in most of the recent Contras, this gun fires two long lines of fire that wrap around each other. While very powerful, it takes a while between shots. This isn't often noticeable since the beams are so long, however if it gets intercepted you lose a lot of time.
- Lock on Thunder: This is the most accurate and fastest lock-on weapon of the original three, and second among all six. It fires up to eight bolts of electricity directly at a target, so it is nearly instantaneous and doesn't need time to move vertically. However it is very weak and cannot go through barriers, so a target must actually be airborne to be hit if there is something in your line of fire. Most of the time this is not an issue, however for the boss of Stage 1 you have to hit targets on top of a mech. With other weapons, the beams would just go above the mech and come down, but the Thunder can't, so it is actually harder to aim.
Weapon Set D
Once you beat Stage 5 you unlock this Weapon Set, regardless of what your rank was. This Weapon Set is ridiculously overpowered, to the point where there is practically no difficulty. All three weapons are very strong, very fast, and fire very rapidly.
- Lightning: Fires a large bolt of electricity directly ahead, killing most weak enemies instantly, and most others in two or three hits. The bolt can pass through enemies, as well as jump between nearby enemies, meaning you rarely have to even aim to take out a group. It's a lot like the spread gun, except with a much higher rate of fire.
- G Bazooka: A long range missile launcher that fires missiles directly head which explode on impact. A very powerful weapon, this is good against bosses and stationary enemies.
- Heaven's Laser: A beam of light comes straight down on the target, meaning the impact is instantaneous and the beam cannot miss the target or get blocked by obstacles. You get the standard four shots and it is about as powerful as any other lock-on, however since they fire so rapidly you'll be able to destroy enemies much quicker than with any other Weapon Set.
Weapon Set E
Like Weapon Sets D and F, this set is very powerful. However, of the six sets, this is by far the hardest to use. There are no rapid fire weapons, nor any that create explosions which hits multiple enemies at once. The reflect laser has potential, however so much of the game takes place in open areas that there are few times where it is practical. This is the best Weapon Set to have against most bosses, however it makes getting through the stages much more difficult.
- Drill: This is an interesting weapon since, while it fires single projectiles, it actually does damage similar to the Fire Whip. The drill fires forward quickly, but slows down as it passes through an enemy, so the damage adds up quickly. This is very useful against large, stationary bosses since the bigger an enemy is, the more time it takes for the drill to pass through them. It is pretty hard to use against large numbers of quick enemies however.
- Reflective Laser: The standard reflect laser used in countless games and some enemies in Neo Contra. The laser fires forward, the bounces off walls. There are a few instances where you can hit enemies that are hiding around corners. However since most enemies run straight at you, this ability isn't as useful as it may first appear.
- Fairy Laser: Once you lock on to your targets (up to six of them) the beams come out in circle around you, and then move to the target in short, quick motions. The beams are fairly powerful, and miss their targets much less often that with other sets (besides D), however they take a very long time to reach the target, so the enemies have much more time to kill you.
Weapon Set F
This Weapon Set has, by far, the most powerful weapons in the game. The set basically combines the power of Weapon Set E with Weapon Set D's ease of use. The Lock-on weapon isn't quite as good as Heaven's Lasers, however it is much better than the Fairy Laser.
- Ripple Laser: If you've ever played Gradius, you know exactly what this weapon is like. Oval-shaped lasers come out of your gun and expand until they are twice as wide as you while moving forward at a fast pace. While these lasers not exceptionally powerful, their speed and width more than make up for it.
- 6V Laser: This is basically the Fire Whip, except that the beam can go across the entire screen. This makes it excellent for clearing out the masses of weaker enemies, and the fact that it is so powerful makes it great for clearing out bosses and larger enemies as well. Most of the time it's actually faster to kill bosses with this than with the Ripple Laser. The only exception is when the boss moves around to fast to maintain your fire with the 6V laser.