Enigmata

Enigmata is a Flash-based, Vertical Scrolling Shooter Web Games developed by Kongregate user Kidsgamez and released in August 2009. A sequel, Enigmata 2: Genu's Revenge, followed in March 2010.

The game is faithful to its roots, with a fairly standard plot and setup. It's Twenty Minutes Into the Future and the Evil Overlord Genu is threatening galactic peace. You play a space-faring Featureless Protagonist on a mission to stop him, aided by the shopkeeper and Text messenger with an internet connection Niko.

You control one of a variety of very spiky-looking fighter craft, and use simple keyboard controls and various Energy Weapons and missiles to shoot at other, equally spiky enemies. Said enemies drop various power ups and cash bonuses with which to buy upgrades between levels. Said upgrades vary wildly, from simple stat bonuses to having unique effects like slowly generating money. You also have a handful of special abilities at your disposal that draw off an energy meter. At the end of each level waits a Boss Fight against increasingly large and powerful warships. You can replay previous levels to obtain more money.

The sequel spices things up by allowing you to aim your ship and weapons anywhere on screen with the mouse whilst still flying vertically through the level, adds a load of new upgrades and skills with heavily diversified effects, and adds an oppressively dark color scheme broken up by colored lights. Oh, and a Mini Game where you collect a bunch of orbs.

Tropes used in Enigmata include:

Attack Reflector: The Reflection Barrier skill.
Barrier Warrior: The blue-lit Tricraft series of ships boast the highest shield ratings. Their low armor and high energy rating also puts them among Squishy Wizards.
Big Bad: Genu. He has a crest that resembles a crescent moon.
Bullet Hell: Some of the bosses can spit out quite a few projectiles.
Bottomless Magazines: averted in the case of your missiles, but you can buy an upgrade that gives you this. It's rather expensive.
Cosmetic Award: This game has a variety of achievements. They actually avert this by offering a monetary reward and "points" needed to unlock better shops.
Critical Encumbrance Failure: Each ship has a limit to how many pieces of equipment it can carry. You can expand this by buying and upgrading the inventory expansion item.
Damage Sponge Boss: The sequel's Cykton Barrier. Doesn't help that it can inflict Cykton Curse on you, which renders your guns all but useless.
Damsel in Distress: You rescue a pink-haired woman named Adriana early in the sequel. She joins Niko in giving you advice.
Dark Action Girl: Clade, in the sequel.
EMP: One skill is called exactly this. It temporarily disables enemy weapons. There is also a type of missile that can do this.
Energy Absorption: The Damage Absorb skill converts damage taken into shield and armor.
Energy Weapon: Your ship's main guns, and most enemy weapons.
Expy: Clade is basically Lash.
Flash Step: The Phase Warp skill instantly teleports your ship to wherever your cursor is.
Healing Factor: The Healing Technique skill.
Implacable Man: It is possible to boost a ship's armor to 5000 or higher. Note that the ship with the highest armor rating defaults at 670. You get an achivement if you pull this off.
Impossible Task: You get an achievement for finishing a mission with a time of zero. Said achievement is called "impossible".
Invisibility Cloak: The Stealth Mode skill. You are also invulnerable while it is active, but you cannot attack.
Jack of All Stats: The red-lit RS series of craft have a fairly balanced set of stats. They do tend to have a greater damage output, however.
Macross Missile Massacre: The Relentless Strike skill.
Mighty Glacier: The orange-lit ships (they have no unifying designation) boast titanic amounts of armor but also the lowest speeds and paltry shield and energy ratings. They do have the most equipment slots.
Monster Clown: Demenus in the sequel.
Nitro Boost: The Warp Speed skill.
Nuke'Em: For a hefty price, you can purchase and use nuclear missiles. They deal incredible damage but have a very slow fire rate.
Poison Mushroom: Enemies often drop negative pickups. These are always marked with an X but are color-coded based on their effect. A number of upgrades directly affect these, whether lessening or nullifying their effects.
Power-Up: Pickups include armor, shield and energy replenishment (both instant-use and kits to be used later), weapon upgrades, missile ammo, and mission-specific drops.
Super Mode: The Guardian of Mana skill.
Standard Status Effects: You can stun your enemies, disable their weapons and freeze them in time. The first two can also happen to you. In addition to stun and EMP missiles, there are ones that can drain health and another that has a chance to inflict instant destruction.
Time Stands Still: The Stop Time skill. Duh.
There Is No Kill Like Overkill: Have you ever played a vertical shooter that had a cast bar?! You get an achievement for having a total of five skills active at once.