"They're gone!" Smith shouted at the second swarm of Agents, standing at the top of the stairs. "We lost! It's over."
In the short time that it had taken him to get there, he was already in his full Agent getup, not a wrinkle in sight. However, his mouth was still bleeding.
The other Agents looked at him, and then turned toward the multiple bodies that were scattered on the bottom floor.
Returning to face him, Agent Johnson asked, "What is the meaning of this, Agent Smith?"
Knowing he had some answering to do, but couldn't do it at the moment, he stood in silence.
"Come with us," said another Agent. Being escorted down the stairs, surrounded by Agents, Smith knew he was in trouble.
Morgana heard a series of stirring sounds and something sliding and lifting open as though underwater, because she was underwater—or goo, to be exact. Sitting up out of pure confusion, she realized it was the hardest time she ever had performing even such a basic action, but not before feeling the warm, viscous glop cling to her. Her eyes hurt, and pain stabbed at them even more as some sort of large, floating machine with blinding headlights pulsed towards her. The hoses snapped off, she was flushed down screaming, and the rest was history.
Smith was back to the empty, windowed office, leaning against the window with one arm overhead. He had been able to convince the Agents that the rebels were extremely well-armed and prepared this time, as well as convincing Agents Brown and Jones that it wasn't their place to interfere with his subject.
"A subject that you failed to deter," said Agent Brown, before Smith, of course, instilled compliance back into him.
The Mainframe, however, wasn't fooled. It queried Smith through the earpiece and right into his mind. Upon accessing everything it needed to—except Smith's human compartment, whom it never even came across—it came to the conclusion that Smith was becoming faulty through some error in his programming, and needed corrective maintenance. After all, it wasn't unheard of that old Programs often started malfunctioning; besides, there were no real casualties: the Mainframe could generate as many Agents as it saw fit. Deciding that Smith needed to be Reconfigured, the Mainframe activated the scrubbing and rebuilding programs in his brain to restore him to the unfeeling, objective killing machine he was always meant to be. The Mainframe also decided to Reconfigure Agents Brown and Jones, to instill added compliance towards Smith.
Except that, Reconfiguration did nothing to alter Smith's human side—after all, if the Mainframe didn't know where it was, how could it destroy it?
After a few moments of silent contemplation, Smith felt like his chest was tearing apart when the image of Morgana appeared in his mind. Recalling every single moment was like being stabbed each time, but he couldn't stop; he missed her too much, and agony brought him to his knees, feeling as low as the ground beneath him. Throwing his sunglasses off and yanking off his earpiece, his head bowed as unprecedented heartache filled his every heartbeat, and he suddenly started crying. Now knowing physical and emotional pain, he knew which one hurt the most.
Commander Harker, Natasha, and Captain Ulrikson were monitoring Morgana's progress after they had extracted all her plugs. Morgana was now laying on a table, with long, thin needles lodged into every neglected muscle. After beginning the muscular stimulation process, it would take Morgana at least a couple more weeks to build up enough strength to walk and perform basic functions. Sedated, she could only see flashes of light and the crew mates occasionally, before dipping back into sleep.
"You know," Natasha said, looking at her unconscious sister. "I still can't believe it ... That was the craziest shit I've ever seen. When I saw that Agent, I thought it was over. Either Morgana was gonna go back to him, or we'd all die. But, he fought for her ... he even killed fucking Agents for her, and in the process, we got away ... I'm sorry, I've been talking a lot about it, I know, but I'm just trying to process it."
"Don't apologize," said Ulrikson. "That's all everybody on this ship keeps talking about, and Zion is dying to know about. This is a situation that I can't understand myself—I understand what it means about love, but not the mechanisms that drove him to love. Unfortunately, this is going to take a long time to process—you, because you're her sister, but Morgana ..." he trailed off, looking into the distance.
Natasha, looking at him expectantly, waited for him to continue.
"Morgana may take months to years," he said. "She might never."
"I won't let that happen," Natasha said, frowning.
"Only time will tell," said Ulrikson. "What I do know is that something feels very strange about our encounter with Smith. This can either be very good, or very bad."
"How so?" Asked Harker.
"This could mean something bigger than you nor I can understand right now," said the Captain. "His behavior is proof that some peculiar event has sent waves rippling throughout the Matrix. We'll just have to wait and see."
Natasha and Harker became pensive at this, and silently wondered at the future.