Agent smiths differ from the other Agents

[cloudwolf]

I don't really count MxO as canon, and so I didn't really consider the Trinity program (partially because I don't know much about it). Even so, the Oracle would know who Neo is because she's got the sight. Besides that, who ran the Trinity program?

Do you have any info on the Trinity Program? I don't know enough about it.

This is the real issue. As much as we like to think big franchises like these are all coherent, they're not. M1 wasn't made with the specifics of M2 and 3 in mind, let alone the comics/animatrix/mxo. These are always things being built on top. Things get a little... sketchier the further from the source they become. What we're doing is taking all the gaps and contradiction and trying to make sense of it. Make theories. Which is fun, but we need to remember there's no magical "right answer" hidden away in some Matrix Bible because really, no-one who made these things thought about what would come after.

As for The Trinity Program, it was basically a plot device to simultaniously explain Neo and Trinity's little "miracles" (i.e. 'we kiss and magically revive eachother' and 'I can fry sentinals in the real and see golden real life code even with melted eyes') as well as justify the motivations of the Oligarch's entering The Matrix.

The Trinity Program (aka The Biological Interface Program) was a centuries long research project into creating human beings with DNA which can be perfectly translated and mapped into Machine code. This would allow the Machines to directly control human bodies, either as spies or who knows what else. This was a solution to the inperfect "overwrite" system which was fundementally flawed (Seraph was able to detect and remove the control programs, returning the hosts to their previous mindset). There was also suggestions it was more to do with Machine curiousity with their creators, which has always kind of been their ultimate motivation (even if they don't see it that way).

Either way, it was what it was. Now, the Oligarch interests comes from the fact they live their existance out in artificial hosts, humanoid androids. When Carlyn heard about The Trinity Project (watching Neo confront Deus Ex Machina) he saw the potential; the ability to interface his now Machine based mind (each Oligarch's mind is housed in a central database within their strongholds then distributed into hosts) with a real human body. Living for centuries without being able to really "feel" anything can be a bitch.

So yeah, Halborn gets wind, enters The Matrix, follows the footsteps of The One, demands the program from the Machines, etc etc Chapter 9+.

It is however worth noting that Rarebit hadn't finalised a lot of the details of the program and had started to consider making The Trinity Program entirely code based and nothing to do with genetic modification. So it's entirely possible The Trinity Program is what was in that cookie.