Shadowcalypse 2 follows Umbra, Upside, and Reverse in their growing resistance against Queen Nebula, who is conquering several galactic systems. However, this game also features a mysterious character who calls himself an Iconoclast. He was born during a blood moon, the symbol of destruction; as such, this character is obsessed with destroying things.
Queen Nebula has uncovered the secret of the mysterious blood moon -- everyone who is born under one gains unique powers. They are known as Iconoclasts, and they are currently being persecuted by Nebula's peacekeeping agency: the Stellar and Tactical Army of Representatives (S.T.A.R.). One of her researchers learns of an especially dangerous Iconoclast by the name of Russell Zhakamovich, who continuously goes insane and causes disaster wherever he goes. Nebula sends a squadron of Cosmotroops out to capture him, then reenters her throne room. A girl named Andromeda, who is doing paperwork the whole time, gets up and sneaks out of the Galactic Tower, seeking to find her one and only crush...
Umbra and his friends Upside and Reverse arrive on Kepler-452b, home to a vast Earth-like civilization. They talk to the planet's governor, Ronriki Sakinz, who distrusts Nebula. He explains that her forces have been spreading throughout the universe, and they need to act -- fast. Just then, Andromeda bashes through a wall into Sakinz's office. Umbra, thinking she is an enemy, fights her. After her defeat, Andromeda warns him of a rogue Iconoclast on the loose, and teleports away.
Umbra continues to search through Sugar Lake City (named for the nearby Sugar Lake, which was known for the strangely sweet taste of its fresh water). He finds an odd poster lying around on the dock. After picking it up, he sees this text:
WANTED: DEAD OR ALIVE. RUSSELL ZHAKAMOVICH. HE IS A TERROR TO THE NEBULIAN SOCIETY. REWARD: FIVE MILLION ZEUROS.
Umbra then shows the poster to Upside and Reverse, the latter of whom states that he has seen him around... especially back in the days when he was still the Sheriff of Sabadones. He is known for terrorizing towns and cities all over the Milky Way galaxy. Upside determines that Russell must be the Iconoclast Andromeda mentioned earlier. Umbra, realizing that Nebula sees Iconoclasts as opponents to her empire, decides to find him and convince him to join the resistance.
The game then cuts to Andromeda's perspective. She is on Io, Jupiter's fiery moon, to inspect a magma refinery for hints about Zhakamovich. However, Nebula has realized that she is gone and has sent Cosmotroops to find her.
Andromeda checks the laboratory, but there is no one there. Suddenly, Russell Zhakamovich himself breaks into the area with blood covering his hands. Andromeda finds out that he killed the scientists at the refinery, and tries to knock him out cold with light energy. Unfortunately for her, he escapes.
She heads to the Galactic CIA office to get help, but there is no one there either. This time, however, she encounters Umbra, who had come here due to a sort of disaster. He lets her help him out, as long as she'll leave him alone afterwards.
Umbra, Andromeda, Upside, and Reverse head for their next destination: Zeusville, the hovering capital of Jupiter. Andromeda states that there has been a history of criminal activity within its boundaries. Reverse scans the area for Iconoclasts, and finds two. One is a male, and the other is a female -- and they are in the Herculean Café.
They charge in, and the signal gets stronger. They finally come across none other than Plato Konrad and Mara Cruor. Andromeda, however, doesn't attack them for a reason she will not explain. Umbra asks Plato if he's seen Russell, but he has no idea who he is. After Andromeda explains, Mara says that she has heard rumors about him, but doesn't exactly know much about him. Upside explains that Nebula is cracking down on Iconoclasts all over the universe, and that seemingly makes Plato a bit angry. He and Mara decide to join them and fight for their rights. Andromeda says she has to gather some gadgets for their use, and Umbra watches as she leaves, somewhat blushing.
Andromeda visits a casino, where creatures of several different species are laughing and gambling. One of the roulette machines has an ion charger, which is needed to trap rogue Iconoclasts like Russell. She tries to sneak it out of the casino, but a group of gamblers catches her, prompting a fight that spreads all around the area. Andromeda eventually escapes with the charger and meets up with Umbra and the others. They board their ship and leave Zeusville.
Reverse is shocked when Governor Sakinz calls him with a devastated look on his face. Sakinz explains that Nebula has overrun Kepler-452b, thus taking total control over the hyperspace trade department. Now, she can conquer other galaxies, eventually proceeding to rule the universe. Umbra asks Sakinz what her current location is, and he replies that she's in the Atlanta Lunar Colony, Umbra's old hometown. Frightened and anxious as to what Nebula could be doing now, Umbra swiftly turns his ship around and leaps into lightspeed.
When the rebels get to the colony, they see that it is being bombed and torn apart. Umbra and Andromeda fight several Cosmotroops in order to reach Nebula, who has finally captured Russell with her pure cosmic energy, which is dangerous to Iconoclasts. They fight her and try to free the enslaved Iconoclast soldiers, but Nebula traps Andromeda with a cosmic lasso, which slowly leads her to fall unconscious. Umbra, realizing that Andromeda is an Iconoclast, attempts to rescue her. Unfortunately, Nebula blasts him away and leaves him to die with the rest of the colony's citizens.
Umbra wakes up in a hospital on Earth. Upside, Reverse, Plato, and Mara try to get him to relax, but he is still angry with Nebula. He notices he feels physically better, so he gets up and storms out of the hospital.
Upside asks Umbra why he is so mad, but he doesn't respond. She says that he can express his feelings however he wants to.
Umbra finally admits that he likes Andromeda, but he just couldn't find the time to tell her directly. He wants to rescue her and help Russell as well, and Upside says that they will... if he's ready.
The rebels reach the Galactic Tower, where they fight their way through security guards and reacue Andromeda and Russell in the process. They enter the throne room, with Nebula waiting for them. She traps Umbra in a cosmic barrier with her, freezing time within it. Nebula finally explains where Umbra's parents have been all his life. However, they were never meant to exist in the 7890s...
They actually met in the 1980s. Umbra was born in 1998, and he lived in that time frame for five years and was sent to the future to live with his "uncle", who was actually his "magnificent nephew" -- 500 generations away from his own time, so far that his relation to him is minimal. Nebula also states that his mag-nephew was an Iconoclast, so she had to send Cosmotroops to murder him.
Umbra is so enraged that he uses White Out to break free of the cosmic barrier and attacks Nebula. They fight for a while, and Nebula seemingly brainwashes Russell to use his power against the rebels. Eventually, Umbra knocks Russell down into the sun, seemingly killing him.
Nebula, knowing that she will deal with the rebels soon enough, forces Umbra and Andromeda into a time hole. She orders a few Cosmotroops to take the others to prison, but Plato and Mara have already escaped.
Umbra and Andromeda land in the current year -- 2016. Umbra tries to explain his feelings for Andromeda, but he stutters. Andromeda tells him not to worry, because she already knows he had a crush on her. In fact, that was why she joined him in the first place. She then kisses Umbra on the cheek, and he smiles a bit.
They then try to decide on their next move, and Andromeda points to a warehouse with the words "ZEON" and "NEEDLENAM WAS HERE" spray-painted at the front.
"Why don't we start there?"