Chapter 25: Confrontation

"You are arriving at the Council Chambers," The elevator's artificial voice chimed out. The doors opened to an unexpected orange hue over the once beautiful gardens. There were bodies of C-Sec officers and geth lying around the area. Immediately on guard, Shepard and the crew raised their weapons and began to slowly advance.

"Shepard to defense team. Come in, Garrus," Shepard whispered into his radio.

"This is Garrus. What's going on, Shepard?" The turian officer responded.

"We've found evidence of geth here in the upper levels of the Presidium Tower. We don't know if any are making their way back down, but watch your rear."

"Acknowledged. Thanks for the heads up." The line went silent.

"Do you think it's Saren?" Ratchet asked.

Wrex grunted in affirmation. "He's been a Spectre for years. I imagine he knows all the secret passageways in and out of the Presidium."

"The Reapers also designed the Citadel, right?" Tali asked, somewhat rhetorically. "Then Sovereign could have given Saren inside schematics."

"Regardless, stay on your guard. There could still be geth or survivors," Shepard said.

Surprisingly, as the crew advanced, they met no resistance, even as they climbed the stairs to the inner chambers where the Council held public sessions. "It's too quiet," Wrex muttered. "My crest is starting to itch."

"My hairs are standing on end," Tali chimed in.

"Wait," Ratchet paused mid-step. "You have hair?" He queried.

Tali gave an exasperated sigh. "You're so tactful."

"Whoops," Ratchet said bashfully. "I didn't mean to just blurt that out… Sorry."

There was a period of silence before finally, Shepard spoke up. "So do you have hair?"

Despite the fact that they could have been ambushed at any moment, Wrex and Ratchet laughed out loud. Tali, on the other hand, was not amused. "Yes, Shepard. I do," She replied tersely.

Still keeping his attention forward, Shepard briefly shrugged. "Sorry Tali, but I was genuinely curious."

The sincerity in Shepard's tone caused Tali's heart to thaw a bit, and she bit back a giggle. "It's ok, Shepard. I've always been curious as to how humans handle having five fingers on each hand. What do you do with them?"

"Oh, there are a lot of uses for five digits," Shepard said automatically, which elicited a snicker from Ratchet, a grunt from Wrex, and a blush from Tali.

"Wow, did it just get hotter in here…" Tali muttered under her breath.

"Lots of uses, I'm sure," Ratchet said suggestively, winking at Tali, who's blush deepened behind her mask.

Suddenly, Shepard seemed to pick up on his verbal gaff. "Wait, that's not– Oh come on! Tali, I didn't mean it like that," He blustered.

But before Tali could respond, Wrex urgently pointed to above them. "Look, the Citadel's arms are moving!"

Everybody immediately glanced up, and indeed, they could see the five massive arms of the Citadel slowly converging in a protective maneuver.

"I can't pick up any radio chatter, even on the Spectre band," Shepard noted. "The geth must be jamming transmissions."

"Wait… Is that the Reaper?!" Tali shouted in alarm as she pointed at a black mass approaching them, getting larger and larger by the second.

"Quick, we need to get up there and override the Citadel controls so the turian fleet can get inside!" Shepard ordered, pushing forward with greater urgency.

"Wait!" Ratchet shouted, stopping dead in his tracks. "I'm picking up Ashley's bio signals!"

"What?!" Shepard exclaimed. "How?!"

"When I modified her assault rifle, I tuned it to her specific bio signals. After Saren kidnapped her, I tuned my scanner to alert me if she's nearby," Ratchet explained. "I just got a ping, and it's getting stronger and stronger by the second."

"She's aboard Sovereign," Tali whispered with dread.

Shepard cursed under his breath. He had promised to himself that he would save Ashley, but they had to keep going forward if they wanted to open up the Citadel and prevent Sovereign from warping the rest of the Reapers in.

"You guys keep going," Ratchet said. "I'm going to board Sovereign and bring back Ashley."

"You can't be serious," Wrex grunted in disbelief. "Did you forget what that thing is capable of?"

"You could die!" Tali exclaimed.

Ratchet shook his head as he manifested his RYNO IV. "We can't leave Ashley on board Sovereign, especially if we're going to destroy it. So I'm going all out this time. Besides, it's always been do or die for me."

Shepard sighed in frustration. "I don't like it, but splitting up is the only solution at this point."

Ratchet nodded. "You guys should hurry. I'm gonna nab one of the hover cars out here so I can get close. Good luck!" He promptly turned and leapt up onto a nearby balcony, letting his omni-tool guide him towards the Council's nearby docking bay.

"Huh, that kid's got a quad, that's for sure," Wrex said, a measure of respect lacing his comment. Tali said nothing, only looking at the spot where she last saw Ratchet, hoping that her friend would be safe.

"We should hurry," Shepard said, taking the steps now three at a time. "We've got to stop– Saren," He growled under his breath as he topped the last set of stairs and saw the traitorous Spectre inputting a final series of commands into the Citadel's control terminal.

In an instant, he raised his gun and pulled the trigger, molten metal flying towards Saren. But with superhuman speed, the turian rolled out of the way, and began to return fire, his free hand holding up a partial barrier.

"Take cover!" Shepard ordered, as the ground crew scrambled out of the line of fire.

"Ah, Shepard and your little band of misfits," Saren called out mockingly. "I was afraid you weren't going to make it in time."

"In time for what?" Shepard demanded.

"In time for the final confrontation. I think we both expected that it would end like this. You've lost, you know that, don't you?" Saren gleefully gloated. "In a few minutes, Sovereign will have full control of the Citadel's systems, the relay will open, and the reapers will return."

"We've still got a few tricks up our sleeves," Shepard retorted, subtly motioning to Tali to ready a tech grenade.

"You and your crew may have survived our encounter on Virmire, but I've changed since then. I've been improved… upgraded, so to speak."

"He let Sovereign implant him?" Wrex muttered under his breath, shaking his head at the rogue Spectre's foolishness.

"You're insane," Shepard retorted, voicing Wrex's thoughts. "You've given up more control to Sovereign!"

Saren laughed maniacally. "After Virmire, what you said about Sovereign manipulating me, indoctrinating me, I couldn't stop thinking about it. But Sovereign sensed my hesitation, my doubt, and he strengthened my resolve and renewed my purpose!"

"You're nothing but a fool," Shepard growled back.

"You are the fool," Saren replied calmly. "The Reapers need organics. I'm sure that even now, if you joined us, Sovereign can find a place for you too."

Tali and Wrex shared a look that said, Is this guy serious?

"Do you even hear yourself?" Shepard asked. "Sovereign's controlling you through your implants!"

A sudden fire seemed to ignite in Saren's eyes, a hint of the Spectre he used to be rising to the surface. "You shortsighted fool! I am the stepping stone to the future! A perfect blend of organic and synthetic. The strengths of both, the weaknesses of neither." Saren paused as if to collect himself. "Join me, join Sovereign, and you too can experience a true rebirth!"

Shepard growled, before suddenly standing up, raising his gun at Saren, the two staring fiercely at each other. "You're talking like we've already lost! But we can still stop Sovereign. Step aside, and this invasion will never happen."

Saren growled in frustration, but stayed his trigger finger. "Don't you see, we can't stop this! Not forever. You saw the visions, the Protheans. The Reapers are too powerful!"

"I can see in your eyes that you haven't lost yet," Shepard said, slowly lowering his gun. "Remember your pride. You can still fight this."

For a moment, Saren's eyes flickered from blue to white as he started to sway listlessly. "Maybe… You're right. Perhaps… AAAGGH!" Saren screamed as he clutched his head, causing Wrex and Tali to jump up, weapons raised. Only Shepard's calm hand prevented them from firing on the spot.

"No," Saren gasped out. "The implants… Sovereign is too strong. It's over for me."

Shepard shook his head. "It's only over when you say it's over, Saren. You can defeat Sovereign."

For a moment, the blue hue cleared from Saren's eyes, and he chuckled. "Heh. I trust you to prevent this madness. Goodbye, Shepard. Thank you." Before anybody could react, Saren raised his pistol to his temple and pulled the trigger, no amount of implants able to stop the bullet from reducing Saren's brain to mush.

The once-proud Spectre swayed from side to side as all motor function faded throughout his body, until finally he toppled over the edge of the railing, falling into the garden below. Shepard breathed a sigh of relief. In the end, Saren had found redemption. But the fight wasn't over yet. He motioned to Wrex. "Make sure he's dead."

The commander then pulled up the override data file that he received from the Prothean AI, Vigil, on Ilos. Crossing his fingers, he uploaded it onto the system. Five seconds later, the console beeped and gave Shepard full control over the Citadel's systems. "I'm in!"

Just then, Wrex fired several shots into Saren's body, which barely even twitched. He called up, "Saren's dead."

"Can you open a communications channel?"

Shepard nodded and tapped a few buttons on his omni-tool. Suddenly, a voice laced with static burst through the comm channel. "This is the Destiny Ascension. Main drives offline. Kinetic barriers at 40%. The Council is on-board. I repeat, the Council is on-board!"

"The Council's in danger!" Tali exclaimed. But before Shepard could do anything about the transmission, Joker's voice broke through.

"Normandy to Citadel. Normandy to Citadel. We've received your distress call and are outside the Andura sector."

"Joker! This is Shepard!"

"Commander? Thank god!" Joker exclaimed in relief. "Nobody's responded for the last few minutes. I talked to Admiral Hackett, and the fleet is ready. We can save the Destiny Ascension, but you need to unlock the relays around the Citadel!"

Wrex, who had just climbed back up, gave a thoughtful hum. "If you try to save the Ascension, there will be massive casualties."

"I'm surprised you care about the Council," Tali noted.

"Ha!" Wrex scoffed. "I could give a pyjak's ass about the Council's wellbeing. But if you wanna take down Sovereign, you'll need every Alliance ship you've got."

Tali shook her head. "But what if the Council dies here, that would throw the entire government into chaos!"

Wrex shrugged. "And risk letting Sovereign bring the rest of the Reapers here?"

Shepard closed his eyes briefly, before hailing Joker again. "Opening the relays now, Joker. We have to save the Destiny Ascension! As soon as the Council's safe, focus on Sovereign. I'm opening the Citadel arms now!"

"Roger!" Joker said, before cutting the line to transmit the orders to Admiral Hackett.

Wrex raised his brow in interest. "The Council had better appreciate this."

Suddenly, the ground began to shake around them as arcs of red energy trailed down the sides of the walls, slamming into Saren's inert body.

"What's going on?!" Shepard shouted.

"It's Saren! Something's happening! His body is moving!" Tali yelled, firing several ineffective rounds from her pistol into Saren's glowing body.

"Bzz… Shepard, it's Ratchet!" The young Lombax's voice buzzed over the comm channels. "Sovereign is emitting a bunch of energy right now, and it's all arcing down the Presidium Tower!"

"We see it!" Shepard responded. "It looks like it's reanimating Saren's corpse."

"I'm almost at Sovereign. Be careful!"

"You too," Shepard responded, before an explosion rocked the platform that he, Wrex, and Tali were standing on, sending the trio plummeting into the garden area with the abomination that had arisen out of Saren's corpse.

"Ugh," Wrex spat in disgust as he dusted himself off. "The Reaper is directly controlling the implants throughout Saren's body."

"But then that must've been over two-thirds of his body!" Tali exclaimed.

"He was more machine than turian," Shepard said wryly. "It doesn't matter. We'll make sure it's dead for real this time."

IIIIIIII

Meanwhile, Ratchet was piloting a hover car straight towards Sovereign's massive form. He took great pleasure in picking out Sparatus' personal hover car. If he was lucky, it would be totally obliterated by the end of this battle.

But as he drew nearer, Sovereign suddenly turned its attention towards the minuscule vehicle racing towards it. Ratchet only smirked. He had faced worse odds before. Sovereign unleashed an ear deafening blast of sound as it faced its challenger, raising one of its tentacles.

Ratchet blasted the windshield off of his hover car and manifested his RYNO. With a yell, he yanked the steering wheel to the side, putting the hover car into a barrel roll and pulled the trigger. "Take this, you hunk of junk!"

Bolts of super charged plasma streaked out of the RYNO's mouth with extreme speed, streaking towards Sovereign with deadly accuracy. Each beam slammed into Sovereign's tentacle, burning deeper and deeper gashes with each impact. Under the heavy fire, Sovereign was unable to fire a particle beam before his appendage was blasted free from his body.

Completely unfazed, Sovereign let loose another mechanic roar before aiming two other particle beams towards Ratchet. But the Lombax was prepared for this. Pushing the hover car into full throttle, Ratchet kicked the driver's door off, and leaned out. He was about 500 meters away, and closing fast.

Manifesting his Alpha Disruptor, Ratchet considered his two remaining cores. Pocketing one, Ratchet overcharged the remaining core. It would probably fry the gun, but he didn't need to fire the last core.

Freeing his mind from all other thoughts, Ratchet gritted his teeth as he felt the thin air around him hum and vibrate with energy. Suddenly, two gigantic particle beams shot forward, slamming into the hover car, completely obliterating it. But Ratchet had already launched himself forward, using the blast's shockwave to propel himself towards Sovereign.

Flying within the range of movement of Sovereign's tentacles, Ratchet found himself racing towards Sovereign's hull at breakneck speeds. Righting himself, Ratchet pulled out his Alpha Disruptor and fired at a point where scans indicated a large hollow interior. The overcharged core unleashed its entire payload in a sudden rush of alpha particles, tearing a massive hole in Sovereign's hull.

His momentum slowed, Ratchet found himself within Sovereign's projected mass effect field, and dropped lightly inside Sovereign's hull. His sensors indicated that Ashley wasn't far. Several hundred meters in that direction. Suddenly, groaning began to echo around the vast chamber, and Ratchet spun around wildly, his Incinerator raised. He was already beginning to feel a light headache from being inside Sovereign, even with his suit completely sealed. It must have been a side effect of indoctrination, then Ratchet would need to be fast.

Jogging towards Ashley's signal, Ratchet suddenly leapt away from the side of the railing he was on as a husk's arm swiped up at him. "Ugh, they're literally crawling on the walls," Ratchet growled. "Well, they won't be able to surround me."

With a yell, Ratchet blasted the husks behind him with his Incinerator and spun in a neat circle, frying the husks surrounding him. Momentarily clear, Ratchet sprinted away until he found his path blocked by a door. Barely pausing, Ratchet tossed his remaining Fusion Grenades at the door, the resulting explosion sending vibrations through the Lombax's feet.

Sliding through the opening, Ratchet turned back and blasted the husk giving chase with another stream of hot plasma. He should be in the same room as Ashley now. As he turned, he saw several geth hovering over what seemed to be Ashley's body. "Hey! Get the hell away from her!" Ratchet yelled as he leapt forward, his Razor Claws at the ready. Several swipes later, and the parts and pieces of sliced geth fell to the ground.

Ratchet quickly moved to Ashley's side and noticed the wires and tubes sticking out of her. He grimaced as he realized that there was a white glow running through Ashley's body, and there were synthetic ports sticking out of Ashley's body where wires were attached. The Reapers had implanted significant portions of Ashley's body, Ratchet realized with horror as he ran a quick scan on his friend.

They had completely violated her in an unimaginable way. Ratchet collapsed to his knees in shock, tears threatening to spill from his eyes, which stared off into space. The moaning echoes of approaching husks slowly brought Ratchet back to reality.

Clenching his fists in a sudden burst of white hot anger, Ratchet smashed his fist into the ground in frustration. "DAMMIT!" He shouted. Just then, several thundering explosions rocked Sovereign, causing Ratchet to stumble forward. "We've gotta get out of here," Ratchet muttered to himself.

Steeling himself, he shook Ashley urgently. "Ash, wake up! Come on Ash!" When there was no response, Ratchet hesitated until the next set of explosions nearly shook him off his feet. "Ok, here goes nothing." With a swipe, Ratchet severed the cables connecting Ashley to whatever Qwark-forsaken contraption the Reapers had devised. He regretted it immediately as Ashley began to violently spasm as she screamed in pain.

"Frack!" Ratchet swore, trying to hold down Ashley, as he yanked more tubes out of the lieutenant's body.

Almost as quickly as it began, though, Ashley's spasms stopped, and she slowly opened her eyes. "… Wha–?" Ashley's voice came out as a weak groan. "Ple… No more…"

And then Ratchet did cry. As Ashley closed her eyes once again and passed out, Ratchet vowed then and there that he would destroy every single Reaper. Hoisting Ashley over his shoulder, Ratchet was surprised at how heavy she was. If his strength wasn't augmented by his armor, he would've had a hard time carrying her. Anger flashed through him again as he realized that it must've been the Ashley's implants. A shudder ran through the young Lombax as it just occurred to him, what if Ashley's been indoctrinated?

Just then, a mass of husks burst through the entryway and rushed into the room towards Ratchet.

A/N: So first, the ending bit of chapter 23 was an outtake that I decided not to use but still wanted to share with y'all. When I finish this story, I'll move it to the outtake section. Also, when people originally asked me if I was going to do a sequel, back when I first started this story, I was pretty excited about it. Then things got busy, and I decided to shelve it. Then I almost decided to shelve this story. But I just finished playing through the Ratchet and Clank 2016 reimagining and then watched the accompanying movie as well, and the plot bunnies are multiplying in my brain! So no promises because clearly, my writing timetable frequently vacations in the phantom zone, but I have plans! I hope you guys enjoyed this chapter.