Part Three

"Neo's still alive."

Gen promptly noticed Morpheus was the only jubilant one in the room over the news that distressed everyone else.

"Correction: he's still alive inside of a leftover Smith copy," Link enunciated.

"He controls him now, Morpheus," Niobe reasonably said, already figuring her husband's intentions. "If you're thinking of going back in there and trying to free him, you're insane. When Smith controlled Bane, none of us realized before it was too late. Neo's as good as dead with Smith in his mind."

"I still have hope," Morpheus protested.

"How do you intend on snapping him out of it?" Ghost inquired. "Neo and Smith are one-in-the-same now. It's not like you can just reboot them like a computer."

A metaphorical lightbulb flashed above Gen's head on Ghost's analogy.

"Maybe we can," she stated. "A virus can reboot itself, if there's enough left of it to get a good kick-start going. Smith used Neo's code as a vessel to return inside the Matrix. What's not to say the reverse can happen?"

"You sound like you can make it happen," Ryuko amusingly observed.

Gen smirked. "With the right technology, I can."

"Well, we're practically swimming in technology here," Ryuko acknowledged. "Just fire something up and take a stab at it."

"The technology we'll require for this task lies in the machine city," Morpheus clarified. "We must plot a course for there."

"Morpheus, think about what you're doing," an increasingly frustrated Niobe tried to reason. "Going into machine city? During a truce? It was agreed we leave them alone, and they would leave us alone."

"Sounds to me like somebody broke their promise," Ryuko figured, "if we've got a psychopath program running around."

It was a thought none of the Nebuchadnezzar II crew considered until that moment.

Niobe's warnings did not go ignored by Morpheus; he knew a plan was necessary before leaping headfirst into a deadly scenario.

Gen proposed plugging her sonic screwdriver into the system, scrambling Neo/Smith's code long enough for Morpheus to try and reach Neo and help him to break away from Smith's control. For it to work, however, Gen needed Ryuko to stand by in the real world and wait for her signal.

She jacked back into the Matrix with Morpheus and Ghost, all while Niobe maintained course for Machine City.

They wandered in the simulation for some time, tracking down Smith.

Link and Sparks eventually pinpointed his location to the rooftop of a skyscraper – the very one that Smith once held Morpheus prisoner and tortured him in.

"I've expected you," the agent said, once approached by his three adversaries.

"Neo," Morpheus addressed without hesitation. "We know you're in there."

"So…you figured out my secret, eh?" Smith remarked. "Yes, Morpheus. Indeed, I have Mister Anderson contained inside this copy – the last to remain after the reboot. Little did they know I would be rebooted, too. And now, with the powers of the One, I feel stronger than before. Let me show you."

The maniacal agent took a step advancing towards them.

"NOW, RYUKO!"

Gen gave the word through the comlink patched within the T.A.R.D.I.S. mainframe, providing the signal she instructed her companion to wait on.

Sure enough, Ryuko followed the command perfectly.

Smith's coding scrambled.

The agent doubled over, seemingly in pain, as his form fizzled in and out, swapped between two different men.

Morpheus stepped towards the shimmering figure. "Neo…can you hear me?"

"Morpheus…I can't…fight it."

"You can, Neo. Smith is not stronger than you."

"He…is…me! He's…too strong! He's gotten…stronger and…stronger…since the machines…tried to reboot…me!"

Morpheus stiffened. "What?!"

"They…never intended…for peace to last! They're…enforcing…a new rule…keeping anyone…from leaving…the Matrix!"

A green glow emitted out of Neo's body, engulfing him and the simulated world around them. Gen, Ghost, and Morpheus reflected from it and soon discovered how all the structures had shifted into nothing but digital codes – the same which Link and Sparks commonly saw on their monitors.

Even Gen, Ghost, and Morpheus themselves were digitized.

They could still make out the figures of each other's avatars but were robbed of any physical traits.

Then there was the burning visage of Smith leering before them.

"This is how strong I've become!"

Again, he seized upon the three interlopers.