Absence Makes The Heart Impatient

Summary:  Neo can’t wait till Smith can join him permanently.
Warning(s):  Disciplinary Spanking of adults using an implement; non-disciplinary erotic spanking; D/s; M/m; very explicit; consensual rough treatment; Potential spoilers all the Matrix movies. Very AU.
Pairing: Agent Smith/Neo

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It had been several days since Smith had last seen Neo, the human having returned to the resistance to make arrangements with his allies there to bring Smith out of the Matrix and to Zion. And they had to do it under the nose of the Analyst, who was seeking out Smith with the intention to destroy him.

Once upon a time, Smith had been able to be anywhere and everywhere, taking over the people in the Matrix. That had been when he'd been an Agent, of course. Now, he wasn't sure what he was. Only that he was connected to Neo and that the human belonged to him...and they couldn't stay here, in the Matrix.

The problem was, the Analyst had eyes and ears everywhere. And several of those had cornered Smith....

***

It had taken a while...a lot of fast talking and getting the crew together...but Bugs finally made a plan with Neo to return to the Matrix and get out the program her fellow human had bonded to. They were on the ship, preparing to enter into the Matrix.

"I need to know who I'm looking for," Bugs said to Neo, before the connection was made. "Who's the program we're bringing out?"

Neo and Smith had been very careful to keep Smith's identity as secret as it was possible to, so it was difficult to tell Bugs who it was. Would she change her mind? He couldn't do this without her, though, so swallowing his nerves down, he answered, "Agent Smith. Although he isn't an agent any longer. I'm pretty sure the Analyst is attempting to destroy him."

Bugs' eyes widened a fraction, but all she said was, "The Analyst had you both under his thumb. Stands to reason he'd target who was left. Do you think you can find Smith?" She began to set it up for them to enter the Matrix.

"He gave me a place to enter that no one, including the Analyst, has access to. Once I'm there, if you can wait, you should be safe while I look for him..." Neo suggested.

Bugs frowned. "There's no way I can join you? You might need help."

"If you go with me, there are more people to catch the Analyst's attention. I want to avoid doing that..." Neo said confidently, even though he wasn't certain it was the correct course of action. He suspected Smith would want him to let Bugs accompany him.

"All right. But if you run into any trouble, you need to let me know." Bugs clearly wasn't happy about it, but she finished connecting them both to the Matrix so they could enter.

"Of course..." Neo quickly agreed.

It didn't take long before they were in a hidden location. "Wait here..." Neo directed, before slipping out into the system to find his mate and master.

***

The Analyst's creations clearly assumed that Smith was defenseless. Backing away, allowing them to assume he was truly cornered, Smith quickly brought a gun to each hand and began to shoot.

Neo had almost reached one of the areas he knew Smith went to when he heard gun shots. He quickly ran in that direction, drawing his own weapons to begin fighting as soon as he saw the enemy.

When the enemy turned to face the new threat, Smith quickly took advantage of the distraction to fire at two of them. He then ducked as a third shot at him, though didn't move quite fast enough to stop the bullet that hit his shoulder. It stung, but he wasn't human. It wouldn't slow him down.

Neo immediately shot at the ones closest to him. He had a vague niggling sensation that at one time, he would have literally been able to dodge bullets and speed faster than those he faced, but... The sensation was very fleeting. He only avoided being shot because he managed to take cover behind a car.

Smith spotted Neo and worry immediately flared within him, seeing the danger his mate was in. Moving at top speed, he shot at the enemy around him, quickly taking out those who would have gone after Neo.

Neo called out to Smith, "We gotta get away from here..." He expected that his mate would know the best place to disappear to where Neo could explain about Bugs being here to retrieve him and take him to the real world.

Smith quickly fired off a few more shots and moved round to Neo's side. He grabbed his mate and quickly pulled Neo into an alleyway that had abruptly appeared and then closed behind them.

Neo quickly followed Smith without argument or question. He knew as soon as it was safe to do so, his mate would stop and question his arrival; and then he could tell him about Bugs. Neo would find out more about the situation he'd run into at that time.

Smith led Neo quickly through various alleyways and through what appeared to be different stores...finding a path through the Matrix away from the Analyst's soldiers.

Neo quietly but quickly followed, keeping his senses aware of everything in case the Analyst showed up and blocked them.

It took a little while, but Smith finally stopped at one of the few safe places he had...though he didn't let go of Neo and remained on his guard. "We should be safe for now."

They were in a small coffee shop, with only a handful of people there. No one seemed to be paying any attention to them, lost in their own world inside the Matrix.

Neo's breathing was rapid, if quiet. He did his best to not act suspiciously. "Bugs found what we needed..." he whispered, knowing Smith would understand that meant they could get him out.

Smith's gaze sharpened. "She's here? In the Matrix?"

"Yessir. We entered in a spot he can't access. I told her to wait for us there..." Neo responded.

"We'll need to move carefully," Smith said. "The Analyst has been tightening his grip on the Matrix."

Neo nodded, swallowing nervously. "He had you cornered...." His whisper was worried.

"I wasn't in danger," Smith replied. "I've survived for a long time." Even if survival the last time had meant being brought back by the Analyst's machinations, he'd still come back.

"He was trying to destroy you..." Neo's voice was slightly disbelieving about the lack of danger.

"He was," Smith replied. "But I've been in the Matrix for longer than him. Longer than you. I know my way around it."

Neo frowned, still worried and unhappy at what he'd viewed as his master being in danger, but not able to refute Smith's claims. "Can we get to Bugs from here?" he asked softly.

Smith nodded. "We'll need to move carefully." He transferred his grip to Neo's shoulder, close to his neck, and quickly led his mate from the coffee shop.

Something about Smith's grip, even if he wasn't technically scruffing him, settled Neo. He quickly fell into a more complacent and obedient mindset, less likely to argue. It made it easier to lead him.

Still keeping a firm, tight grip on Neo, Smith began to lead the human back through various parts of the Matrix. He was moving the way a program moved, rather than a human, so it was a much faster form of travel.

Neo just kept close and quiet. It was a little disconcerting, moving the way they were; it went against what now felt natural to him. His complete trust in Smith enabled him not to get confused and lost, though.

It took a little while, but they finally reached the location where Bugs had been left.

She straightened immediately and looked towards them. "Everything all right? No one chasing you?"

"The Analyst. But we've lost him for now," Smith replied.

"We can get him out now, right? He'll be safe?" Neo couldn't hide his worried hope.

Bugs nodded. "The same way all of us got out." She held the pill out to Smith.

The former agent took it, without hesitation.

"See you on the other side." Neo gave Smith a hopeful, excited, if slightly nervous smile.

Smith nodded as he swallowed the pill...which did the job it was meant to. Like Morpheus, the pill disconnected him from the mainframe of the Matrix, allowing him to break free and enter the computer on the humans' ship.

As soon as she knew it had worked, Bugs disconnected both her and Neo from the Matrix so they could wake on the ship.

Neo blinked, allowing himself to adjust to being out of the Matrix again. As soon as he felt able to move, however, he was disconnecting himself so he could go to the ship and find Smith.

The pill had allowed Smith to integrate himself into the mainframe of the ship, but much like the other programs who had been freed, he was able to manifest on the ship in a holographic form...and he did that almost as soon as Neo had disconnected himself. "We're both free of the Matrix now," he said, his voice soft.

Neo nodded, his smile bright. "We're both safe..." he said, before turning towards Bugs. "Thank you...."

Bugs just nodded. "When we get to Zion, we can figure out a ship for you to enter the mainframe and make your permanent home," she said to Smith. "For now, you can use this one."

Neo grinned. "When he enters the mainframe, that will enable him to interact with all the others like Morpheus? Move around the base, instead of being stuck in one location?"

"Exactly," Bugs replied. "The ship's mainframe will basically be his home. No one else allowed without his permission."

"But he can leave to go to the public areas of the mainframe?" Neo asked.

"Yes. Just like the rest of the programs," Bugs confirmed.

"Great!" Neo grinned even brighter, looking at Smith.

"We can enter this ship's mainframe now." Smith spoke the words in a firm voice, giving an order rather than making a suggestion.

Neo blinked. "Is it ready right this second?" he asked Bugs. "Am I able to go into his space?"

"You can use this ship's mainframe until we reach Zion," Bugs confirmed.

"Okay..." Neo looked for where he'd need to connect.

Bugs showed him to the area, which was in a more private part of the ship.

"Thank you..." Neo smiled again, quickly connecting himself and slipping into the system.

By that time, Smith had entered the mainframe himself. He was limited in how he could change the environment, as this wasn't his ship, but they could touch each other.

Once Neo was completely connected to the mainframe, Smith moved to the human and wrapped his arms around his mate, kissing him hard and deep.

Neo sunk into Smith's arms, leaning into the kiss, and opening up for his master eagerly.

Smith pressed deeper and harder, lightly nipping at Neo's lips. Then, he pushed his tongue into the human's mouth. At the same time, his hands roamed over Neo's body...removing clothing...stripping him.

Neo whimpered softly at the domination, giving in, and submitting immediately. He helped where necessary for Smith to remove his clothing; accepting the other man's tongue by moving his own out of the way and opening his mouth further; and shifting so that every part of him was vulnerable to Smith's whims and decisions.

As soon as Neo was naked, Smith roamed his hands over the human's body, squeezing and rubbing down his arms. He pressed Neo against him, so that the human could feel his own erection straining against his pants.

Neo shivered; felt himself slipping into the needy, obedient mindset he always fell into when it was just him and Smith and his master took control. "...Sir..." he whispered, his voice needy.

In response, Smith lightly scratched his nails down Neo's back and buttocks before he bore the human down to the ground. He could only manipulate the surroundings a bit, but it was enough to cause a soft surface to form...almost like a bed they could lay on.

Neo shivered again, whimpering as he felt himself lowered. The change of hard floor to soft surface was a little disorienting, but he trusted his mate completely. He closed his eyes and let Smith control his body, at least until they were situated. It would allow the other man to make the 'world' as he wanted without Neo getting motion sickness.

Smith changed the room to how he wanted it, more of a bedroom with soft blankets and sheets than the hard, wooden floor it had been. Then, once it was done, he let his fingers graze over Neo's member; leaned down and engulfed one nipple into his mouth.

Once Smith had laid him down and out like he wanted, Neo opened his eyes again... Just in time to throw his head back with a low grown, baring his throat, at the double attention to his body. He opened his legs instinctively in a show of submissive trust, leaving himself open to Smith's wants and desires. Smith could do anything, pleasurable or painful- possibly both- and Neo would take it.

Smith replaced his mouth with his hand, tweaking the nipple, and closed his teeth around Neo's neck. He didn't bite...didn't pierce the skin...but he could feel Neo's pulse, his life force, fluttering against his lips, against his teeth.

Neo whimpered and groaned again, his member twitching in Smith's palm at the show of dominant possession. His nipple was a hardened pebble against Smith's fingertips. "...Master..." he breathed out, in a begging tone.

Smith grinned at the begging tone, giving Neo's member a gentle squeeze before beginning to firmly stroke it. "What do you want?" He liked hearing his human beg. Wanted to hear more of it.

Neo whined softly. He didn't exactly know what he wanted. Just that he needed Smith. "...Need to feel you." His voice caught. "All of me needs to feel that you own me...."

"Every part of you belongs to me. I own all of you." Smith began to suck on Neo's neck, so that he'd leave a mark behind. He continued to tweak Neo's nipple; let his nails run over his human's member.

Neo whimpered and squirmed at the harsher treatment, his member becoming harder as he became more aroused. "...Need to be sore for you... Ache for you... Master," he begged.

Responding to the words, to the arousal, Smith grazed his teeth along Neo's throat and then bit; not hard enough to draw blood, but hard enough to be felt. He moved his hand towards Neo's other nipple, beginning to twist and tweak it.

Neo let out tiny sobs of aroused need, his member twitching again and getting larger. His whole demeanor was complete submission, willing to accept any physical action Smith chose to do; comforting or punishing, he didn't care, as long as he could feel his master's control.

Smith moved his hand away from Neo's member, leaving the human at the edge of arousal, and parted his legs enough to expose his backside. Then, he began to smack it...very quickly coloring the skin to a warm pink.

Neo let out tiny whimpers at the sting, slowly transitioning to soft cries as the sting turned into a hot ache. He left his legs exactly as Smith put them, wanting, and needing the stern affection. "...Please..." He begged for more.

In response, Smith began to smack a bit harder and a bit faster. He continued to tweak and twist Neo's nipple. He then lowered his mouth to the nipple and engulfed it, grazing his teeth against the sensitive nub.

Neo moaned softly as the ache began to last more than a few seconds past the smack. He'd feel it for a while after Smith stopped, as long as he remained in the frame. He let out a tiny sob at feeling his nipple scraped and arched his back so his nipple pressed more firmly into his master's mouth. His begging was becoming incoherent...but he was still begging.

Smith grinned against Neo's skin at the sound of the begging and gently bit the nipple in his mouth; not hard enough to break the skin, but enough to be felt. And he began to smack Neo's inner thighs, turning them the same shade of red as the rest of his human's bottom.

Neo quivered under his master, reaching a point where he could only react physically and in non-verbal vocalizations. He couldn't even beg, though it was clear he would if he'd been able to formulate a coherent word. His entire focus was on Smith. He was on the edge of dropping.

Smith raised his head and then licked his way to Neo's other nipple. He began to suck and bite the other nipple, even as he continued to swat his human's thighs. His other hand began to firmly stroke and lightly squeeze Neo's member.

"M... Master..." Neo breathed out, in a moaning whisper. He was unable to stop himself from thrusting into Smith's hand. He felt completely out of control.

"Mine." The word was a low growl, barely recognizable as a word...but Smith's actions were driving home his possession; that Neo belonged entirely and utterly to him.

"Yours..." Neo's voice quivered, with a hint of tears. He had never felt so completely that he belonged.

Smith sucked and bit the nipple in his mouth until it was reduced to the same state as the first. Then, he returned his attention to Neo's neck...closing his teeth around the skin there. And he called lube to his hand that he coated his member in before pushing into his mate.

Neo quivered, groaning softly as he felt his mate push in, stretching him. He felt so full, but he needed more. He let his head drop back, exposing his jugular. He was completely at Smith's mercy.

Smith began to thrust into Neo, going deep and hard. When his human exposed his jugular, Smith closed his teeth around it; not biting or piercing the skin but holding his mate's life in his hands.

At the complete show of dominance and ownership, at feeling that Smith held his life in his hands, Neo dropped. Fast and hard. He couldn't have waited for permission if he'd tried, his orgasm tearing violently through his body in long spasms.

Smith's own orgasm washed over him, triggered by Neo's. His whole body slumped over Neo's as he rode out the waves. Then, once it had receded, he carefully pulled out of his mate. Placing a hand on Neo's cheek, he began to call his mate back.

Neo slowly became aware again, following Smith's voice and touch. As soon as he was more focused, he began to quietly cry, small tremors coursing through him. Everything had been very intense, and it was difficult to regain control over himself and his emotions. The difficulty made him nervous... almost afraid. He looked up at Smith helplessly, trusting and needing his mate to help him.

"You're safe." Smith spoke the words in a low, reassuring tone. He summoned a cloth and ointment to his hand and began to carefully treat the marks he'd left on Neo's body. While he enjoyed seeing the marks he'd left on his mate's body, taking care of Neo felt just as important to him as being possessive.

Neo nodded wordlessly, obviously relaxing as Smith took care of him even if he was spooked. The only reason he wasn't clinging to Smith was because his master needed to be able to freely move to treat him.

Smith was gentle and thorough as he treated the marks left from their rough claiming. Once he was done, he summoned a blanket to his hands and carefully wrapped it around his mate.

Neo shivered and snuggled as close to his mate as Smith would allow. "...Sorry I'm being a baby..." he whispered, slightly ashamed that his emotions had got away from him.

"You react in the way you need to," Smith responded. "It isn't being a baby." He wrapped his arms tightly around Neo.

Neo nuzzled closer, taking comfort from his lover. "I love you so much..." he whispered.

"I love you too." Smith stroked his fingers through Neo's hair; cuddled his lover tightly. "I've got you. And you're mine."

"Forever!" Neo declared, in a fervent promise. "...Can still feel where you were in me..." he whispered a few seconds later, his voice happy.

"Good," Smith said, with obvious feeling. "I want you to feel me for as long as possible."

"I want that too..." Neo smiled crookedly, cuddling closer still. "Feel it as long as possible while I'm here and remember when I'm out there...."

"And now that I'm out of the Matrix, you can come to me any time you want or need to," Smith said. "And I can come to you as well, even if I can't touch you physically outside of the mainframe."

Neo nodded, cuddling. "Maybe someday... We'll figure out how to make bodies that you can go in and live with all the abilities of people. Where you can feel and interact like you do in the frame, but outside of it." Neo pondered the idea.

"There is every possibility it will become common in the future," Smith agreed. "But for now, there is no immediate danger."

"Now that you are free, there is no danger!" Neo asserted.

"I wouldn't say we're entirely free of danger, but we're at least safer here than staying in the Matrix," Smith said.

"We're able to be together and not be kept apart," Neo whispered, snuggling close. "I won't be able to be so careless with what I do, since you'll be able to see me and stop me..." he continued innocently, realizing he was telling on himself, but feeling he needed to confess. There shouldn't be any secrets between them and now that Smith was free of the Matrix, chances were very high he'd be told by someone else. Neo would rather confess on his own.

"What have you been doing?" Smith's voice was calm, if very serious. Getting angry wasn't really his way; at least not anymore. A lot had changed since he'd been brought back from wherever it was programs went when they died.

"I did some missions for the base so they could free you quicker. I wasn't as careful as you would expect me to be..." Neo sighed softly, knowing he'd probably earned himself punishment.

"What happened?" Even though it was likely Neo had earned himself a punishment, Smith wasn't going to act until he had all the information.

"To get this ship, we had to clear some areas of debris. I... did a few things that almost got me hurt," Neo reluctantly admitted. "Almost got buried alive once ...."

"Were you actually injured?" Smith couldn't have hidden his concern if he'd tried. He was pretty sure he would have noticed any injuries his human had received, but even so, he wanted to make sure.

"I... I sprained my ankle, but not badly. I'm back to normal now..." Neo bit his lip. "I don't want you to worry... Almost didn't tell you... But I know you'll find out anyway and I needed you to hear it from me."

"Did anyone check your ankle?" If they hadn't, if no one had checked Neo for any injuries, Smith would make sure that someone did now.

"I had one of the healers make sure it wasn't worse than I thought. I knew you'd want me to make sure. Would have insisted if you knew what happened..." Neo smiled crookedly.

"I would have," Smith confirmed, running his hands over Neo's back. "I'm pleased with you for making sure you were checked over. However, you shouldn't have taken those actions in the first place. And I am going to punish you for it."

Neo sighed softly, nuzzling against his mate. "I kinda thought you would. But I still wanted to tell you myself... felt wrong to hide it, even if I'm in trouble now..." he whispered.

"I'm glad you told me. It was the right thing to do." Smith pressed a gentle kiss to Neo's shoulder. He held his mate for a few more moments and then carefully shifted Neo into position across his lap.

Neo swallowed hard and reached back so Smith could hold his hands in place. He didn't want to accidentally block if it became too much to handle. "I'm sorry I upset you..." he whispered again. 

"You put yourself in danger. And you got yourself hurt. That is what I'm upset about." Smith moved the blanket out of the way, enough to expose Neo's bottom without moving it from the rest of his mate's body. Then, he summoned a hairbrush to his hand.

Neo whimpered as he felt the cool air on his bottom and sensed the hairbrush moving to his master's hand. He didn't ask to not be punished, though. He'd known he was doing something he wasn't supposed to do.

Taking a firmer grip on Neo, Smith lifted the brush and brought it down firmly; not unbearably so, but enough to be felt. And then he brought it down a second and third time.

Neo had still been slightly dropped from their love making. It took very little time at all for him to begin crying; entirely from guilt and shame that he'd upset his master, though the smacks did hurt. "I'm sorry," he choked out.

"I know you are," Smith replied. "But you need to change your behavior. You need to be safe, even if I'm not there to make you behave."

"I... I know... Need to... Should have..." Neo agreed. His voice was shaky through his tears.

"I don't expect this to happen again." Smith finished one circuit of strokes with the brush and then began a second one.

"N... No, sir. Won't! I'll be so much careful! Do what is 'spected!" Neo promised, in a tight voice, before sobbing and slumping, accepting the punishment. He deserved whatever Smith chose to do and he would never fight. Taking unnecessary chances with his life wasn't allowed. He wasn't alone anymore. He didn't need to throw his life away. His master didn't want that.

Smith finished up with a final few strokes from the brush and then stopped. He quickly gathered his mate into his arms, hugging Neo close and tight.

As soon as Smith had pulled him up, Neo was snuggled as close as he could get, clinging to his mate. "Love you..." he said, in a small voice.

"I love you too." Smith kissed Neo's neck and cuddled him close and tight. "And if you ever do something that will endanger you again, I will spank you longer and harder," he promised.

"Yessir..." Neo snuggled close. "I'd deserve it," he reluctantly admitted.

"You would. But you'd also be forgiven...and comforted...afterwards," Smith said, stroking down Neo's hair and over his back.

"...You take care of me..." Neo whispered, then nuzzled against Smith.

"Always," Smith replied. "You belong to me. You're mine."

"Forever..." Neo sounded content. He felt so safe with his master.

The End