Upgrades is the 3rd scene in The Matrix Reloaded, it refers to the title given to the Agents who are harder to fight.
The scene begins with a single knock on the outside steel door of the compound in which Neo and others are having a Crisis Meeting. It is then answered by a disgruntled Corrupt. We then hear the voice of Agent Smith without seeing his face. he states that he is looking for Neo. Corrupt has been instructed to let no one uninvited in so then tries to tell Smith that he has never heard of Neo. He does not know it is Smith has he has never heard him before and cannot see that it is an agent due to extremely bright car lights from behind Smith. Smith then presents a gift to Corrupt to give to Neo in return for Neo's favor of setting him free. Corrupt then takes the package and tell Smith to "piss off".
Neo then appears in the room as if he had sensed the presence of Smith. He asks who it was and then is given the gift by Corrupt. We find out that the package had an agent's earpiece in. This indicates to Neo that agents are coming and therefore tells Corrupt and Wurm to "retreat to their exits". They leave as Neo stays back to protect the retreating Resistance members.
We then hear a knocking on the metal door as if someone is breaking it down. Sure enough we see agents; Thompson, Jackson and Johnson break down the door and enter the room. They then talk to themselves as if they where one person. They finish each other's sentences and answer their own questions. Once they have decided that they are going to neutralize Neo they proceed to fight him as they believe he is "only human".
After Agent Johnson making eleven moves against Neo, all of which where parried by Neo, Neo then makes his first move against The agent. it is caught by Johnson which seems to surprise Neo as this move would usual have hit a agent and not have been caught. Neo then utters the Title of the scene "Hmmm, upgrades" to show his intrigue to these new and improved agents, seeing them as a harder difficulty in the game that he will inevitably win. All three agents then continue to fight Neo simultaneously. Neo is winning from the start and all throughout.
After the fight we see Neo outside as he uses his powers to fly straight up into the night sky, warping surroundings which indicates the stress placed on the Matrix whenever something abnormal happens.