Hello again, new chapter time! I'd just like to start off by saying I'm doing everything in my power to fill the plot holes Bioware originally gave us (What's this random panel in this random part of the Citadel, aren't the arm controls in the Citadel Tower?) and I hope my new resolution makes more sense, whether or not it's happy. I'd also like to thank those who reviewed my first chapter (koryandrs, Nightstride, and kill-phil), helped bolster my confidence in this story, and I'll try to stop using run-on sentences Nightstride (sorry commas are just so easy to use). Also, I know many will be disappointed, but there's no romance stuff in this chapter (I'm sorry it just didn't fit :/ ) Maybe next chapter, but who knows what will happen. Anyway, as usual I own nothing, Bioware does, and I hope you enjoy my story!

Ch. 2: The Citadel

London, Earth

Commander Shepard

Time seemed to slow down as Shepard continued the suicidal charge with several other soldiers. He watched in horror as Harbinger blasted a laser at the nearby soldiers; they disappeared into dust as the laser continued on its path, towards him. Shepard quickly summoned as much biotic energy as he could and charged towards one of the several Marauders guarding the beam. Harbinger narrowly missed Shepard, and it let out a synthetic roar as the Commander crashed into the Marauder. Shepard killed the Marauder instantly and smashed his fist into the ground, sending out a Nova attack to knock the other Marauders back. He then ran the last few steps into the beam before Harbinger could fire another blast.

Citadel

Shepard was blown out of the beam into a strange keeper tunnel. He grunted as he stood up, and surveyed the room around him. He grimly noticed a seemingly endless number of Collector pods, many already filled, hanging on the walls. He forced himself to focus and started moving towards the Council Chambers. If his memory served him correctly, the Citadel arm controls were on the central control panel in the Council Chambers.

He felt major déjà-vu. 'Saving the Galaxy almost seems repetitive.' He thought, then quickly scolded himself. He had a job to do, and everyone in the galaxy, from Human to Asari to Geth, was counting on him.

"Shepard, wait!" Shepard turned around to see Anderson come out of the beam and approach him. "Thought you might need a little help up here, Shepard." Anderson said with the faintest of smirks until he noticed the Collector pods.

"Shepard, are these the Collector pods you described in your reports?" Anderson asked while looking in horror at the walls around them.

"Yeah, I bet they're trying to build another Reaper in here somewhere. They must beam humans up here, place them in pods, and process them into a new abomination..." Shepard shook his head. He let Anderson compose himself and then started walking on past the keepers and the pods.

"Is there anything we can do for them?" Anderson asked, keeping his voice low.

Shepard looked at the pods, and shook his head. "We could try to open them but… There's just too many, and we need to open the Citadel arms. If don't get those arms open anyone we do save will die anyway."

"Your right, let's get to the Council Chambers ASAP then." Anderson attempted to move a bit faster.

Shepard noticed he was limping a bit as they continued on. He must have been hit trying to get to the beam, but he seemed to be moving so he could still fight.

Shepard opened a door, surprised they had found the Council Chambers so easily. Of course, that wasn't all they found.

"I underestimated you Shepard." The Illusive Man smiled darkly. He was standing right in front of the central control panel, with several ATLAS mechs and Cerberus soldiers guarding him.

"I warned you, control is the means to survival, control of the Reapers, and of you if necessary." The Illusive Man continued.

"And how exactly will you control me?" Shepard glared at him, but then noticed what leverage the Illusive Man had.

The Illusive Man's minions brought forward several members of Shepard's team, past and present. Cerberus soldiers had guns pointed at the heads of Liara, James, Javik, Jacob, Jack, Zaeed, Kaidan, and Samara. They had their hands tied to their heads and had gags over their mouths.

"How…" Shepard started to ask, but The Illusive Man interrupted him.

"You of all people should know I have many sleeper agents, Shepard. It wasn't hard to get your teammates to follow orders that came from you, or at least orders they thought came from you." The Illusive Man smirked sinisterly. "Just look at how easily I can control you using the right methods! I can do this with the Reapers as well."

Shepard shook his head. "Controlling me is a lot different than controlling a Reaper, Illusive Man. You can't exactly use hostages against the Reapers."

"Have a little faith Shepard." The Illusive Man took out his pistol. "I remember a time when I thought your shortsightedness ruined our chance for human dominance in the galaxy... but now? Now, we can control the Reapers! We can use them as our weapons to subdue the other races, to bring humanity its true destiny!"

"Listen to yourself, you're indoctrinated!" Anderson yelled at The Illusive Man.

The Illusive Man chuckled darkly. "You can lie to yourself all you want, Admiral, but it won't change the fact that you're scared. You're afraid of the powerful leader humanity could become! We could advance more than the past 10,000 years combined! We could build a beautiful, human-controlled galaxy, with the Reapers subject to our every whim! Humanity could even surpass the limitations of our galaxy, and colonize other galaxies! Don't you see this is the way humanity must evolve?"

Shepard looked right at him, and stated defiantly, "You're playing with things you don't understand, with power you shouldn't be able to use. That power cannot be given to anyone!"

The Illusive Man paused for a moment, then spoke. "I… don't believe that. If we can control it, why shouldn't it be ours?"

"Because, we're not ready. We don't deserve it!" Shepard explained.

The Illusive Man glared at him. "And when will we be ready Shepard? When will we deserve it? When will humanity achieve its destiny if we have leaders like you, afraid to seize an opportunity that is laid out for you!? No, this is the way humanity must evolve Shepard, this is how we secure a beautiful future for us and our children!"

Shepard shook his head. "No, you're just doing what the Reapers want. If we destroy them this ends today, but if you're right, how do you know you can control them forever? What if they break free, what will happen to your beautiful future then?"

The Illusive Man frowned. "I shouldn't expect an alien-lover to understand. You've saved far more alien lives than human lives anyway; it's truly embarrassing you were the first human Spectre. I've had enough of this, so lay down your weapons or your team will die."

Shepard reluctantly let his weapon fall to the ground. Anderson set his own weapon down more gently.

'There has to be a way out of this.' Shepard thought, then noticed sometime big. All but two of the squad mates that Cerberus had captured were biotics!

'This might help us.' He thought as he raised his hands to his head.

The Illusive Man continued to ramble his Indoctrinated nonsense as Cerberus troops moved Shepard and Anderson to the captured group. Shepard looked hard at each biotic, and gave a determined look to James and Zaeed, and hoped that they got the message. As far as Shepard could tell they had been unconscious until moments ago, and their implants should still be working. A Cerberus soldier moved his holo-cuffs towards Shepard's hands, and Shepard yelled 'NOW' and blasted the soldier away with his biotic power. The other biotics did the same, and soon all of Shepard's team was free of their holo-cuffs, grabbing the Cerberus troops weapons, and taking cover.

"You'll ruin everything I've done for humanity, Shepard! It's time for you to die!" The Illusive Man yelled as he got inside his own custom-built ATLAS Mech. The other ATLAS Mechs followed him and went to attack Shepard and his team...

Author Endnote: So, did you like the new word-battle with the Illusive Man? Is it epic or what? I always thought we should actually be able to fight the Illusive Man, and I think this would've been the most logical way to do it. Also, for any Indoctrination Theory fans, I decided to give that little Easter Egg about the seemingly different laser Harbinger fired. I'm not actually doing anything Indoctrination Theory like, but I thought why not give a little shout-out? Anyway, what will happen to Shepard's team? How long will it be until Shepard can get to the Citadel arm controls? What will happen when the Crucible actually connects to the Citadel? And what about Tali and the Normandy? Stay tuned and review! :D

P.s. If anyone says that Cerberus was destroyed at Cronos Station, I have an explanation. Several missions in the game are you attacking Cerberus bases, and I'd like to theorize he had another base somewhere closer to Earth that he used to get troops and get onto the Citadel. I highly doubt that The Illusive Man would walk around without some kind of elite guard at least, so why not ATLAS Mechs?