Throughout The Matrix franchise, Keanu Reeves' Neo often overpowered his enemies as The One, but even so, there were a few fights he lost. Neo's narrative journey was one of a man learning to embrace his own inner power and tap into the mental fortitude needed to break free of the control of the Machines and bend the Matrix to his will. In the end, it's revealed that the real strength came from the union of him and Trinity (Carrie-Anne Moss) all along, but Neo first had to embrace his calling as The One to get there.
Neo didn't exactly immediately tap into his powers at first, and even after becoming The One, there were still quite a few fights in sequels where he was overpowered when a new opponent confronted him with a new set of skills or strengths. There were, at least, certainly a few fights he would have lost if not for a fortuitous twist at the very end. Other times, a fight came in waves, where he decisively lost the first round, both combatants stopped, then Neo won in the second round. Either way, there were a handful of fights in The Matrix movies that Neo didn't win cleanly, and even a couple that he lost.
6 Neo vs. Morpheus: First Kung Fu Fight (The Matrix)
Neo's first real fight in The Matrix quadrilogy was the one where he and Morpheus (Laurence Fishburne) went head-to-head in a dojo simulation to test out Neo's newly-ed kung fu abilities. Though Neo eventually flashed some of the innate power that made Morpheus think he was The One in the first place, the vast majority of the fight - certainly the first few rounds - was more like a cat playing with a mouse. It initially seemed as though Neo was landing a few punches, but it soon became clear that the master was simply testing Neo to see how far he could go. Neo's inexperience and doubt of his own abilities held him back, limiting what he was able to do against the much more experienced and battle-hardened Morpheus.
5 Neo vs. A Hundred Agent Smiths (The Matrix Reloaded)
It could be argued that this was the only fight in The Matrix movies that Neo decisively lost. Matrix Reloaded's face-off in the abandoned lot was a good test of Neo's power in of seeing how he'd evolved since the first movie. Where the Neo of The Matrix had a hard time handling even one Agent Smith (Hugo Weaving), the Neo of The Matrix Reloaded had a fairly easy time holding his own against multiple Agent Smiths. However, the tide of the fight turned when Agent Smith, whose fighting style evolved in the Matrix movies, started making dozens of clones and Neo soon found himself fighting a hundred different Agent Smiths. Once he grabbed a lead pipe that he wielded like a bo staff, it helped, but he was still outnumbered and overpowered. In the end, Neo only escaped by flying away.
4 Neo vs. Super Agent Smith (The Matrix Revolutions)
This Matrix Revolutions fight, like so many themes of the entire Matrix franchise, was a bit of a paradox: in order to win, Neo had to lose. And while he technically won in the sense that he achieved his aim of seemingly defeating the Machines, he first lost the physical fight, and then he lost again by letting himself be subsumed by Smith. If he had not had the realization at the end of fight that the only way to win was to allow Smith to take him over in order to gain access to Smith from the inside, it would have ended differently.
The fight was evenly matched for a while, but once they started trading punches in the air, the power dynamic changed. Agent Smith all but ended it when he suplexed Neo from the sky, smashing him into the ground so hard that they made a crater. Until he lost the fight intentionally, he was most definitely losing the fight against his will.
3 Neo vs. Bane/Agent Smith (The Matrix Revolutions)
Neo ultimately defeated Bane (Ian Bliss) in the Matrix Revolutions fight aboard the ship Logos, but it was a Pyrrhic victory at best. Bane (who was possessed at the time by Agent Smith) took Trinity hostage and threatened to kill her, but the clever woman turned off the lights, giving Neo a chance to escape. It ended up with Neo scuffling with Bane-Agent Smith, and Neo eventually overpowered his opponent and wins. However, it came at a high price: during the fight, Bane-Agent Smith shoved a live power cord into Neo's face, electrocuting and permanently blinding him in the process.
2 Neo vs. Agent Smith - First Subway Fight (The Matrix)
Like a number of his battles against Agent Smith, Neo was pretty clearly losing most of the fight. This is the case in the final fight between Neo and Agent Smith in The Matrix, which was really broken into a series of fights (or rounds, if one prefers). The subway fight is a brutal fight between Neo and Agent Smith, with both trading Herculean blows, and for a while Neo, newly hatched as The One, is even able to hold his own. Agent Smith then finds another gear within himself that the inexperienced Neo is not able to yet access. The only reason that Neo escapes is that the two fall onto the tracks right as a subway speeds toward them, with Neo escaping just in time and leaving Agent Smith to be hit by the train.
Agent Smith was hardly dead, though, and merely possesses the body of the conductor to continue the fight. This time, Neo outright flees, realizing he can not defeat someone who can not die. However, he's caught by Agent Smith and his fellow agents and fatally shot. While Trinity's kiss resurrects Neo, it's only then that he is able to tap fully into his powers as The One and stop the agents. Had it not been for Trinity, Neo's fight with Agent Smith would have ended in the ultimate loss of death.
1 Neo vs. The Trainman (The Matrix Revolutions)
Neo's fight against the Trainman (Bruce Spence) in The Matrix Revolutions is a quickly-forgotten fight against the backdrop of Neo's iconic fights with Agent Smith. However, it's surprisingly one of the few fights in which an opponent beats Neo–or at least escapes completely unscathed. Neo meets the Trainman shortly after the events of The Matrix Reloaded, waking up in the purgatory of a way station designed as one of the ubiquitous subway stations in The Matrix franchise. As someone loyal to the Merovingian, the Trainman, who initially appears to be a harmless homeless man, soon confronts the newly-awakened Neo and overpowers him. The fight is a short one, but it ends with the Trainman punching Neo into a wall and then making his escape.
