The Matrix is an unquantifiable cultural phenomenon — on the one hand, it is a crucial juncture in the evolution of CGI; on the other, it deals with some of the most mind-bending philosophies available in a popular movie. It's surprising to see how popular the film series still is, given that a sequel has now been green-lit for production.
Although several elements in The Matrix can be associated with the iconic 90s anime, Ghost in the Shell, the Wachowski Sisters' final product belongs only to itself. All the characters that fans know and love (or hate) may not necessarily be how they appear, however. Some of them have shown tendencies beyond the code-scripts that bind them — here is a list including characters who don't always stick to their part.
Acts Like A Villain - The Oracle
The Oracle takes on the appearance of a kindly neighborhood grandma — always ready with a plate of hot cookies and some smart advice. However, it is clear that her intentions surpass any single individual. She claims that she wants to help Neo, offering platitudes about his role in the game.
At the same time, she knowingly sends him on journeys from which he rarely returns unscathed. It might be argued that The Oracle exists without bias, but this could also mean that her "empathy" is simply a means of manipulating the Prime Program into satisfying the requirements of the Matrix.
Actually Heroes - The Agents
The Agents are nothing more than anti-virus programs, built to weed out any unwanted anomalies within the system. They do their job with efficiency, even if they take a small amount of sadistic pleasure from it.
In the specific case of Neo, the Agents are not exactly guided by firm hands (Smith's corruption spreads through them), but in general, they are incredible cleaners. Vast networks like the Matrix cannot survive, or even be stable, without a team of workers erasing errors wherever they arise.
Acts Like A Villain - Morpheus
Morpheus plays a paternal role in the trilogy, from introducing the fledgling Neo to the revolutionary structure of Cyber Martial Arts to having his back when the Council hesitates in placing their faith in the One. Nevertheless, his motives are inherently selfish. Morpheus obeys his own drive, his exact destiny, and no other.
The only reason he believes in Neo is because of the prophecy that claimed that he would be the one to find the One. If Morpheus discovers that he was meant to kill Neo, the story would have played out very differently.
Actually A Hero - The Architect
The Architect comes off as a cranky old man simply because he exhibits a degree of misanthropy. This can be partly excused, though, given how human greed and envy resulted in the planet being destroyed.
The Matrix is not a centralized intelligence, or in other words, AI consciousness is not limited to a specific object or location. Still, The Architect can be considered a program that is able to make decisions outside the network. Given its refusal to discard humanity, it plays a heroic role far more than it does a villain.
Acts Like A Villain - Persephone
Persephone is The Merovingian's jilted wife, whatever that means for a couple of programs. She despises the way her husband treats other "women", channeling that righteous anger into helping Neo and his team. At the end of the subplot, however, she walks towards The Merovingian with a smirk on her face, and turns his own words back against him, "Cause and effect, my love."
This shows that Persephone doesn't quite care about actually aiding the heroes as much as annoying her husband. For more evidence, consider what she demands from Neo in exchange for her help.
Actually A Hero - Cypher
Cypher is weak, annoying, pathetic, and lot of other things, but he is true to himself. It might be a stretch to call him a hero, but his actions, self-serving though they may be, at least display his rigid set of beliefs.
Cypher cannot tolerate the squalor of the Nebuchadnezzar, nor the slop they eat every day, nor the constant threat of Sentinels looming overhead at all times. Instead, he musters up the courage to do what's best for himself, even though he does it in the creepiest way possible.
Acts Like A Villain - Commander Lock
Commander Lock, Niobe's current beau, claims to be on Zion's side. But his thoughts, words and actions betray his motives, showing that his patriotism is twisted into his own ego. Lock hates Morpheus, for his previous dalliance with Niobe as well as his rebellious nature.
He especially does not enjoy it when Morpheus pulls ridiculous stunts and somehow succeeds, like when he brings the One to Zion. To Lock, the victory of Zion against the Sentinels is worthless if he cannot get his personal ambitions taken care of at the same time.
Actually Heroes - The Machines
The Machines have not had a fun history with humans. Not a real shocker, considering how humans treated the first AI that they themselves created, as detailed in The Animatrix (2003). When the machines chose to build their own nation, 01, they began to thrive, quickly becoming the most powerful government on Earth.
Humanity opted to destroy them, but were comically outmaneuvered — so they decided to blacken the sky, isolating their enemies from essential solar energy. Instead of murdering all humans in revenge, the Machines chose the higher path: it keeps them alive in a peaceful world, far from the harshness of the real one.
Acts Like A Villain - Neo
Neo is the One, the accumulation of every structural anomaly inherent to the third version of the Matrix. He has one role: to allow the destruction of Zion, so it can be repopulated again, allowing the cycle to continue.
Instead, Neo runs through the wrong door, because he was completely fine with the final death of all humanity as long as he could spend a few measly seconds with his lover. Although everything works out at the end, it clearly exposes Neo's ode to romance as a deep selfishness and total lack of concern for actual people who were going to die.
Actually A Hero - Deus Ex Machina
The Deus Ex Machina is an indecipherable part of Machine City. It is as yet unclear if it is a single program or the summation of the Matrix itself. It doesn't quite believe Neo the first time, at least until the latter claims that he is the only way to get rid of Smith.
It is clearly a gentle consciousness, albeit given to bouts of "rage", because it does not seek to destroy people, but rather find some way to ensure a symbiotic relationship between human and machine. To be perfectly honest, there is nothing stopping it from leaving us to die alone on a dead world.