Rise

by OrbitingTheSun

Shepard found the Illusive man's base in ruin. Something had escaped, but the battle for Earth called and Shepard couldn't look any further into the incident. It's been a decade since and Shepard's crew is being killed off by a mysterious figure. It claims to be a member of Cerberus, an organization thought dead, but what are its real motives?

Don't own Mass Effect

Prologue

The Systems Alliance fleet was prepared for a fight. The Illusive man's base was supposedly one of the most protected places in the galaxy. But today it would fall. Cerberus could've maybe once been an ally but now they were indoctrinated, they had the idea they could actually control Reapers. And after Horizon no one could say anything in Cerberus's defense. It was when the fifth fleet approached the Illusive man's base they found it silent. All fighters on deck, as though no one got the chance to even get in them. The Alliance vessels where in shock, this had to be some sort of trick, some kind of trap. The fleet waited for a while to see if anything was happening, but they were met with nothing.

When John Shepard entered with his squad he found the base covered with bodies. Centurions, Phantoms, and Engineers littered the floors. Some looked like they suffered from bullet wounds, but strangely some looked like they had died from being pummeled to death. Broken necks, smashed ribcages, and all sorts of mangled limbs were found on many of the dead. Shepard continued on treading carefully, guessing that this was probably the result of another Cerberus project gone wrong. Shepard passes by more hallways seeing more dead. As Shepard walked up the staircase to Illusive man's main office he found a figure in black that was sprawled out on the stairs, lifeless. Shepard thought the figure looked familiar, and when he turned the corpse around he found it to be none other than Kai Leng. Shepard took a moment to observe the scene Kai Leng had no bullet wounds, and the wall next the stairs looked like it had dents in it. It was as though some person had grabbed a hold of the Cerberus agent and hit him repeatedly against the wall until he died. Shepard never liked Kai Leng, especially after Thane's death, but Shepard knew he was Cerberus's best. If something killed him in that manner it had to be powerful.

Shepard told his squad to be ready when they got to the entrance of the Illusive man's main office. EDI, Shepard, and Ashley with weapons in hand stormed the main office ready to face whatever was waiting for them. They were met with only an eerie silence of a vacant room. In the middle sat the Illusive man in his chair with his head hung down, infront of him was a hologram of a pristine Earth spinning on its axis. Shepard came up to the Illusive man to find he had stab wound in his stomach, he had bled out already.

Shepard didn't have the time to find what caused the Illusive man's death or the deaths of the people in the base. The battle of Earth was going to start soon this Cerberus monster could wait another day, EDI found the Prothean VI and Shepard couldn't dwell to long on what just happened. One thing still disturbed him more than the killings at the base, when Shepard found the Illusive man slumped on his chair he could swear that there was a faint smile on his face.

A few hours earlier

The Illusive man was disappointed, and relieved. Disappointed that he personally would not see the day when humanity was the dominant species in the galaxy. Relieved that his goal was still possible with Harper.

The Illusive man watched his security moniters from his chair awaiting what was coming. Harper was making quick work with the security personal. The Illusive man felt a sense of pride as Harper past by Centurions with ease, but there was still time before he would get here. From the hologram projector in the office a floating red cube appeared before him.

"Sun Tzu, I need to thank you for what you did. You've insured that my dream will live on in him."

"No thanks is required, I was simply doing my duties Illusive man. When I saw that your behavior strongly indicated indoctrination I acted as you would want me to. I am of course an expert on strategy, being an Enhanced Offensive Intelligence."

"Are you getting all the data he will need when he goes off on his own? Harper is only a few hours old", the Illusive man asked.

"It has been done, Harper will be aptly prepared", responded Sun Tzu.

The Illusive man looked again at his monitors; Kai Leng was making a last stand with Harper. The Illusive man knew that he only had a minute or two at the most now. It was good that Sun Tzu woke up Harper now; the whispers in his head had turned to shouting. The Illusive man didn't even realize his indoctrination until Sun Tzu alerted him to it, and acted accordingly. He remembered that it took him a while to accept he was indoctrinated but, now he was restraining himself to keep from giving in. Everything would be over soon.

Deep in thought, the Illusive man was interrupted by the sound of Kai Leng's body getting bashed into a wall outside of his room. Then his door opened, and a man entered. He was in a larger, pure white version of Centurion armor, the only color came from an orange Cerberus symbol was on his chest. His face was covered by his Centurion helmet hiding any emotions he may be displaying. The Illusive man stood up to take a long look at Harper, and Harper did the same to the Illusive man.

Harper slowly reached his hand out to touch the side of the Illusive man's face for a moment, with his other hand he turned on an omni blade. The Illusive man tasted blood in his mouth and slumped back in his chair, the deed had been done. Harper kneeled down to watch his father die. Blood gushed out of his stomach wound pouring on the floor. The Illusive man only had a little life left in him. Harper gave one last look to the Illusive man, and said to him,

"You will not die here father, for I am you and you are me. As one part of you goes into the darkness another comes into the light"

The Illusive man was then left in his office by both Sun Tzu and Harper. With his last ounce of strength he ordered that his hologram projector, show him a view of an unspoiled Earth. The Illusive man stared into it, as the voices in his head were silenced one by one. The black abyss of death actually seemed appealing to him. Harper would continue everything he could not accomplish. Harper was his ultimate creation, a part of him that would live on after death, he would make humanity the ones above all others. He will be the future.

New Story, the idea's been in my head for a while, I'll get into the AU elements next chapter.