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In Games

While The Matrix: The Path of Neo follows the story of the Matrix trilogy relatively closely, the ending battle between Smith and Neo was deemed "unworthy" to a computer game, since it would require the player to lose. So they replaced it with a battle against the MegaSmith.   

While the battle plays out as it does in The Matrix Revolutions, once Neo sends Smith crashing into the ground forming a crater, the game changes to the MegaSmith scenario with all the Smith clones banding together with pieces of debris to form a giant Smith. In order to defeat this, the player has to fly Neo into the MegaSmith’s mouth, destroying the boss from the inside.

While Smith was defeated at the end of the trilogy, he resurfaces in The Matrix Online as a virus which overwrites certain characters. So far, there have only been 4 known infections with the first two being takeovers of human/machine liaison characters, Agent Grey and DifferenceEngine with both starting to show emotional responses and a vehement interest in finding Mr. Anderson. The third infection involved a bluepill named Shane Black who was the able to spread the virus to others causing an outbreak. While they were eventually cleansed, Black continued to be violent and had to eventually be killed. The most recent resurgence of the virus was during the third anniversary events when a group of men in black appeared and started fighting with redpills. However, they suddenly disappeared soon after with the announcement that it had found a new and more dangerous form.
 

Appearances in Movies

The Matrix

In the first Matrix movie, Agent Smith is a program inside the Matrix itself with the purpose of finding and eliminating as many 'redpills' as possible. Accompanied by Agent Jones and Agent Brown, he is seen in the opening scene of the movie arriving at what appears to be an ordinary crime scene, until it is soon revealed that Trinity is inside, hacking into the Matrix to find information on Neo. Taking control of the situation after informing the lieutenant that his men were already dead, Agent Smith sends his own men in to take down Trinity, but she escapes across the rooftops and reaches a public phone box. This is the first display of the Agents' power to switch between any body jacked into the Matrix, as he switches into the body of a passing truck driver and uses his vehicle to smash into the phone box in a last ditch effort to kill Trinity before she can escape. Even though he fails, he instantly regroups with his men and blends into the background.

The second time we see Agent Smith in the movie, he's arrived at the Metacortex building and is looking for Thomas A. Anderson AKA Neo. While Neo tries to escape at first, he is soon apprehended and taken into custody by the Agents. Even though Agent Smith is a computer program, while interrogating Neo, he shows a display of satisfaction when he takes away Mr. Anderson's ability to speak and plants a bug in his system assuming he will now turn Morpheus in.

'Find them and destroy them.'
Upon returning from a visit to The Oracle, the crew of the Nebuchadnezzar become trapped in a supposedly safe abandoned building by the Agents, as well as a team of SWAT, thanks to a tip off by Cypher. During the escape, Morpheus sacrifices himself to give Neo time to escape. Unbeknown to him however was Agent Smith's mission to capture and torture him until he gave up the password to Zion. As an Agent and therefore far more powerful than any 'redpill', Agent Smith quickly defeats Morpheus and takes him to a skyscraper where he is to be held prisoner until he has given up his code.

While the methods the Agents use to crack Morpheus are cutting edge, they prove to be unsuccessful with Morpheus showing no signs of revealing his code. After one particular outburst, Agent Smith orders his fellow Agents out of the room and disconnects his ear piece thus disconnecting himself from the rest of the Matrix. He then delivers a vitriloic and passionate monologue to Morpheus describing how much he hates humans and how he sees them as a virus rather than mammals. However, he is interrupted by Agent Jones and Agent Brown who alert him of Neo and Trinity's rescue attempt as well as questioning him about why he disconnected from the Matrix.

While Agents Jones and Brown chase Trinity and Neo, Agent Smith bides his time and waits for them to run for a hardline so they can escape back into Zion. While Morpheus and Trinity get through fine, Agent Smith warps into the body of a homeless man who was sleeping in the station and shoots the phone with his Desert Eagle. Having a definite hatred for Neo as being the only human who has escaped him, they face off in the empty train station. While surprised at Neo's ability move as he does, Agent Smith still manages to gain the upper hand before letting his anger take control of him, giving Neo enough chance to launch Smith into the roof of the train station and backflip onto the platform just in time for the train to pull in, hitting Agent Smith with all its force. However, almost immediately, Agent Smith inhabits the body of a passenger stepping off the train which causes Neo to flee in search of a hardline.

Neo's panic proves to be his downfall as he runs directly into Agent Smith, who had taken control of the body of a resident in a nearby block of flats. Firing several shots in Neo's stomach, killing him on the spot. However, Neo is soon revived after a kiss from Trinity and he becomes much more powerful than any of the Agents, who all start firing at Neo. When this turns out to be useless, Agent Smith runs down to confront Neo but finds all his attacks blocked with one hand and gets kicked down the corridor. Neo, now able to manipulate the Matrix, leaps inside Agent Smith and destroys him.

The Matrix Reloaded

At the start of the movie, Smith, no longer an agent of the Matrix, tracks down a secret meeting between the captains of the Zion fleet but instead of attacking the humans, he simply delivers ‘a gift’ to Neo. The gift is his earpiece, which sends the message to Neo that he too is no longer a slave to the machines. Soon after, the redpill meeting is interrupted by new and improved Agents causing the humans scatter to the nearest available hardlines and while all are seen escaping, Bane, a member of the Caduceus, encounters Smith who takes over his body, producing a double who slips out of the Matrix.
The Burly Brawl

While in control of the body of Bane, Smith attempts to murder Neo by stabbing him in the back but is interrupted and forced to leave him for another time. Soon after, back in the Matrix, Smith encounters Neo after his second meeting with The Oracle and tells him that after his defeat, he was meant to return to the Source and be erased, but instead he went against his programming and is now living as a ‘free man’ inside the Matrix system. However, this has left Smith without a purpose and so he is in fact not as free as he believed he would become. This prompts the Burly Brawl where Smith and his many clones take on Neo. At first Neo fights them off but eventually the numbers become too great and trap him on the ground, giving the original Smith enough time to start taking over his body. Neo proves to be too strong, however, and manages to use the last of his strength to fly away.

Smith is then not seen until Neo and Morpheus take the Keymaker to open the Source. While opening the door, the Smith clones descend on the corridor from all angles with one clone managing to shoot the Keymaker, killing him, but not before he could open the door to allow Neo inside. Soon after, in the real world, the battle between the human fleet and the machines starts with a disaster when an EMP is fired early causing many ships to instantly become powerless and therefore easy to destroy. Bane, however, manages to be the single solitary survivor and ends the film attached to a life support machine on the opposite side of Neo.

The Matrix Revolutions

Since the development of Smith’s cloning powers, it seems he had been using them to spread throughout the Matrix much like a virus and in the opening scene of the movie, it is shown that he has taken over a large majority of the humans connected to the Matrix itself thus protecting himself from the machines who want him deleted. Smith even goes as far as to clone himself into the body of The Oracle. This gives him the ability to see into his own future where he sees himself defeating Neo in one final battle.

'Mr. Anderson, welcome back.'
With Neo fighting on behalf of the machines after bargaining for Zion to be spared, he re-enters the Matrix to finally defeat Smith who now is equal in power to Neo. Having seen his victory, Smith does not use any of his clones and instead tackles Neo one on one much like he did in the first film. While fighting, he reveals to Neo that it was him who taught him the meaning of life: ‘The purpose of life is to end.’

He continues to fight Neo, eventually gaining the upper hand and leaving Neo in a severely weakened state. It is here that Smith questions Neo’s motivation to continue fighting even though he knows he can’t win, to which Neo responds ‘Because I choose to.'  This lack of real justification confuses and angers Smith who continues to beat down on him before finally taking over his body and becoming all powerful in the Matrix. However, as Neo was jacked into the Matrix through the Deus Ex Machina, the machines are able to connect with Smith and delete him from the system.

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