- In the distant future, Earth is suddenly threatened by a mysterious phenomenon which revolves around weapons malfunctioning at military facilities around the world. The cause of these mysterious incidents are crystals who have the ability to use the weapons against humanity. This is referred to as "Crystal contamination". As a result of these incidents, an elite military organization known as "V.C.D.", or Vanguard for Crystal Destruction, is formed. The V.C.D. is armed with a series of fighter planes known as the Fighting Thunders, and most of them are present at the V.C.D.'s command ship, the Bellwether, with Richard Maxwell as acting captain of the ship. The player is one of those Fighting Thunders, referred to as "Raiden" by Richard Maxwell, and their mission is to defeat the crystals and the contaminated weapons across the planet.—Anonymous
- 17 years had passed since the war with the Crystals had begun. The Vanquish Crystal Defense, or VCD, is awaiting orders to launch the Fighting Thunders into battle to assist the North American army which is under attack by the Crystals. On the VCD flagship, the Bellwether, Captain Richard "Max" Maxwell and Eshiria Portman grow impatient over the order, since they consider a Crystal contamination a bigger problem than other situations the VCD has dealt with.
Fighting Thunder is eventually given the order to assist the North American army in fighting back against the Crystals, destroying Platon, a contaminated battleship in the process, and Max and Eshiria receive word from the Middle East branch that there is a major Crystal activity in the region. Eshiria notes that the energy signatures are similar to the ones detected in North America. The VCD eventually stumbles upon a cave of Crystals, and Max has a shipment of the Crystals sent to a French shipping port at a Large Hadron Collider facility, under suspicion that they may have a sign of intelligence. After Fighting Thunder destroys the contaminated drilling machine Great Horn, they escape from the cave and Max orders an SOS call to the port after having doubts from his superior, Helga Lindenbaum of the international peace council. Max's suspicions were unfortunately proven right, as they Crystals attack the port, and the Crystals also have the ability to upgrade any machinery and weapons they contaminate, as shown with the submarine Kraken transforming into a hovercraft.
Max orders Fighting Thunder on a mission to defend the LHC facility from the Crystals, expecting there to be a massive presence. Once again, his suspicions are proven true, as they have overrun the facility in an overly military fashion and also hypothesizing that there may also be a core giving the Crystals orders. Fighting Thunder eventually clears the contamination from the facility and fends off an attack from mounted cannon carrier Spice Birds, but a surveillance drone steals the Crystals from the Bellwether and takes them to a pirate mercenary named Valbarossa Hawkeye, who plans to ship them to an unknown facility.
Max sends out Fighting Thunder to pursue Valbarossa and retake the Crystals, and Valbarossa orders the flagship to attack. After the flagship's defenses are disabled, the Crystals suddenly begin to contaminate ship's command bridge, the Blow of Hornet, upgrading it with an energy cannon to destroy Fighting Thunder. After sinking the pirate ship, Valbarossa, revealed to be a woman, joins Max and Eshiria aboard the Bellwether.
Valbarossa reveals her client to be Lieutenant Walter Erick Campbell, the head of VCD's weapons development division and a researcher in the mysterious organization SHIFT. Fighting Thunder is then given the order to raid the facility where Campbell is located. Earlier, Campbell had revealed to Max that through SHIFT's efforts in utilizing Crystal energy, Bellwether and Fighting Thunder now exist, also claiming the war effort is dependent on him. As Fighting Thunder attacks the facility, Campbell once again reiterated his stance on SHIFT's continued research on Crystal energy, denouncing the Montevideo agreement that banned it. However, Max tells Campbell about the dangers of Crystals and the research on it due to him being on the front lines, since they had contaminated Valbarossa's ship earlier. Fighting Thunder then destroys the facility and begins its escape through the facility's cargo route, but not before Campbell sends out his mobile weapons Messiah to spite Max and Fighting Thunder.
After the attack on the SHIFT facility, Campbell was arrested by the VCD, and Helga has confirmed Max and Eshiria's hypotheses on the Crystals, eventually culminating in the conclusion that one Crystal is relaying information on the others and the machines contaminated, comparing it to that of Carl Jung's theory on collective unconscious. She then orders Max and Eshiria to prepare to launch into outer space to prepare for a counteroffensive on the Crystals' mother planet, destroying the contaminated space debris retrieval colony Angel in the process.
VCD eventually arrives at the mother planet, and find there is no life and has been completely overrun by the Crystals. Detecting large energy signatures deep within the planet, Max and Eshiria order Fighting Thunder to infiltrate the interior of the planet to investigate, in which they confront and destroy the planet's guardian, Humpty Dumpty. During the battle, Eshiria notes that the atmospheric composition is the same of that as Mars, and the data relayed to the Bellwether by Fighting Thunder reveals that the Crystals are made of the same composition as water. It's also revealed that the Crystals' invasion of Earth was not a normal invasion, and that their true motives involved resetting Earth by annihilating all life on the planet through polluting the environment and contaminating their machinery before cleaning up the pollution and making the planet inhabitable again.
Depending on the player's performance, the game will end with either the VCD returning home and seeing a planet which looks like Mars, only to find that it's Earth having been reduced to a lifeless red rock, or the Bellwether unable to return to Earth due to damages sustained during the final battle, but with Earth celebrating its victory over the Crystals with the destruction of the elusive core Divine Rampart, and the Crystals melting into liquids forming seas and rivers in their home planet, and Helga sending a rescue ship for the crew that will arrive within a month, and Max cautions the crew to stay vigilant in case another attack occurs.
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