“	They use bots now, skinned as normal people, which means they are everywhere and you never know who to trust. ”
― The Matrix Resurrections

"Bots" are new Programs in the The Analyst's rebooted and redesigned version of the Matrix, which have replaced the earlier Agent programs. While Agents relied on raw power and extreme mobility, Bots rely on camouflage and vast numbers. Typically dormant, they live out fake scripted lives interspersed among the Bluepill humans in the Matrix - but when activated into "Swarm mode", dozens to hundreds of Bots will instantly descend on a target.

Replacing the Agents in a new Matrix

In the old system, the Machines used a relatively small number of super-powered Agent programs, who could "body hop" between the shell of any Bluepill human already plugged into the Matrix - making them simultaneously "everyone and no one". Killing an Agent only killed the current body it was overriding, causing the body to revert to normal while the Agent downloaded again into a new one nearby. There were still a few drawbacks to using Agents, however: while they could potentially turn into any Bluepill, they couldn't be everywhere at the same time, and their super-powered abilities made them somewhat conspicuous (even in their token guise as some sort of high-ranking government secret agents).

The Analyst's new Matrix is based more on manipulating the humans inside than on direct, blunt control - and particularly through use of digital media permeating society, thus making it more easy to control (with iPhones, social media, etc.). Embodying this shift in strategy, Bots are camouflaged as normal Bluepill humans in the Matrix, living alongside the coppertop humans. There are so many thousands of disguised Bots in the new Matrix that there are essentially always a few in most public places (and even private places such as individual businesses), making it all the more easy to spy on the real humans in the simulation. Some Bots, called handlers, are assigned to spy on and manipulate specific people - maintaining much more subtle control by posing as friends and even family members.

Bots replaced Agents similar to how Agents replaced the earlier Seraphim. The original guardians of the simulation in the Matrix Beta Versions, they were eventually deemed to be too powerful and conspicuous, so they were replaced with the downgraded Agents. Seraph was a former Seraphim who not only survived as an Exile, but eventually sided with The Oracle against the system. The Bots are, in effect, a continuation of this trend: individually weaker Programs who can fit in better with humans, to draw less attention to themselves until force is needed.

According to The Analyst, Bots are not only less conspicuous than Agents, but simply cheaper: he says that "cloning Agents over a coppertop" isn't as effective as just "saturating a population" with Bots interspersed everywhere. Apparently having Agents body-hop between different coppertop humans (who are themselves an energy source) simply wasn't as energy efficient.

"Swarm mode"

“	They're everywhere. Such a pain, cloning Agents over a coppertop. Far more effective just to saturate a population. And, bonus, swarm mode is sick fun! ”
― The Matrix Resurrections[src]

Bots operate on the strategy of permeating the new Matrix with thousands of disguised bots to spy on the humans within it. If a genuine threat appears such as members of the Resistance, all of the dormant Bots in a large area can be activated - switching to "Swarm mode" - instantly transforming into a literal army at a moment's notice, attacking in waves like a zombie horde. Activated Bots' eyes turn black, and fill with glowing green Matrix code.

Bots operate on a more "quantity over quality" strategy than Agents did, and camouflage over raw power, resulting in several trade-offs. Individually they aren't as fast or powerful as Agents, nor are they as well-armed (they can't just carry around guns all the time in their fake lives), but they make up for this with overwhelming numbers and the ability to hide in plain sight. Military and police Bots do carry guns, but they are less common.

Another distinction is that Bots cannot body-hop the way that Agents did: they actually do have their own scripted lives, which they act out all the time, instead of shifting to other people. As a result, when Bots die they die permanently, and their bodies simply dissolve into Matrix code (in contrast, Bluepills who die in the Matrix, including those possessed by Agents, will leave a corpse behind when they die). It's possible that this was intended as a safety feature after Agent Smith went rogue and modified his body-hopping ability to start copying himself like a virus. Even the revived Agent Smith discovers that, while he can still body-hop, he can no longer copy himself - further indication that the reformatted Matrix as a whole has been reprogrammed to remove this ability.

Despite the fact that when Bots die, they die permanently, when in swarm mode they will unquestioningly go on suicide missions. When Neo and Trinity attempt to escape through the city streets on a motorcycle, the Analyst activates a mega-swarm throughout the entire population - including ordering all dormant bots in nearby high rise buildings to hurl themselves out windows, essentially turning them into gravity bombs from the force of impact.

Trivia

• Bots seem to be the living embodiment of how much the Internet has changed in the two decades since the first Matrix films, with the rise of social media and algorithm-based manipulation - literally thousands of algorithm "bots" pretending to be "real" on social media are attempting to manipulate people, all the time. Instead of the Internet being a new and mysterious but somewhat distant thing - like the Agents - the Bots saturate the new Matrix, just as society by the 2020s is now permeated with social media and algorithms. In 1999, the Internet/Agents impacted powerful and important things such as new online banking, but not every second of the day, but by 2021, people are connected to social media literally every second of the day with iPhones they carry around for even minor interactions.
• There was some confusion when The Matrix Resurrections was first released whether "Swarm mode" is a new form of Agent-programs copying over Bluepill humans, but on closer inspection, dialogue in the film states that they are just "bots" (sentient Programs) embedded in the simulation but pretending to be Bluepill humans. The Analyst specifically says that they're not "cloned over coppertops" the way that Agents are.
• Actor Daniel Bernhardt was intended to reprise his role as Agent Johnson in The Matrix Resurrections: although he indeed filmed for it and was featured in the film's interviews and marketing, his scenes were removed from the final cut of the film. While his exact role in the fourth film has yet to be confirmed, it is possible that his scenes would have given further explanation on how the Agents were replaced by the Bots in The Analyst's rebooted Matrix (i.e. possibly appearing with The Merovingian and the other Exiles who managed to survive The Analyst's purge).
• Most of the large crowds of Bots in "swarm mode" scenes were actual people, not CGI. The climactic chase scene through the city streets in The Matrix Resurrections frequently included shots with 70 real stuntmen and extras playing bots, and at times, crowds of up to 300 real people running through the streets.