For simplicity, here’s some basic definitions to terms I will refer to:


The System—that which operates and controls the Matrix.  Various programs that are a 
part of it, including the Architect.

Free programs—programs not doing what they are suppose to, operating independently of 
the Matrix.


Let’s start with a question that a critic considered a plot hole.  
Obviously this critic didn’t think too much about what they were watching.


WHY CAN’T NEO STOP AGENTS THE SAME WAY HE STOPS BULLETS?


The One is apparently an illusionary tool used by the System to control those it can’t 
control by normal means, ie the Matrix.  Since The One is created by the System, its
 powers are defined by the System—Neo’s powers are limited to what the System allows 
The One to do.  

There are three main ways to kill a human—projectiles, explosives and melee combat.
 Neo can stop projectiles.  He can also detect explosives, evident by the elevator 
conversation on his way to the Merovingian.  We also know Neo can sense what is going 
on, even if he can’t see it, as shown in the opening sequence when he ‘knows’ that 
agents are coming and Smith was approaching their meeting spot.  Oh, there’s also poison
 but Neo would of course see that as well.  This leaves melee combat.  We know Neo is 
vulnerable from the Burly Brawl and from dropping blood in the Chateau, though quite 
difficult to beat.  After all the System wants him to be powerful, to provide hope for 
the Others and to be able to make his way to the Source against those who do not know 
about the prophecy (or care, in the Merovingian’s case).

*NOTE*  Apparently the ability to stop bullets is a learned power, something the 
previous Ones may not have been able to do.  Otherwise the Merovingian, who has 
survived other Neo’s predecessors, wouldn’t have his henchman try shooting.  It also 
makes his statement “Okay, you have some skill” bear more meaning in this light.


DO THE AGENTS KNOW ABOUT THE PROPEHCY?

No.
The purpose of an agent is to keep the rebels under control.  The System expects 
rebels to exist, so it implemented agents to keep the rebels from running amuck within
the Matrix.  A system of control.

If the agents knew about the prophecy, it is unlikely they would refer to him as the
‘anamoly’ in Reloaded, or even had tried to fight him.  They were alone with him and 
there was no reason for anything but honesty.

--It is possible that the agents are faking ignorance to give the illusion of control
(common theme).  After all, if they ran from The One every time, their role would be 
reduced and rebels would have much more freedom behind The One.  Plus, the rebels 
might get suspicious if the agents acted differently--

However the biggest evidence that the agents don’t know is Smith.  It is clear Smith
does not know what Neo is or about the prophecy.  As an agent, Smith was intent on 
killing Neo.  Having no control of Neo’s mind, the System can not guarantee that he 
would have lived if shot, so Smith as an agent was doing what all the agents were 
attempting—to kill him particularly by shooting, oblivious to Neo’s true role.

But when he is freed, the conversation he has with Neo shows his ignorance.  He still
refers to Neo as “Mr. Anderson,” showing that he thinks nothing more of him.  Also, 
Smith was clearly surprised and confused that Neo rose after Smith shot him, saying
that what he saw was “impossible.”  If he knew of the prophecy, but didn’t know Neo 
was The One, by this point he should put 2 and 2 together and thought “Well, maybe 
this guy is The One.”  Nope.  


OKAY, SO WHY DOESN’T NEO JUST DESTROY THE AGENTS LIKE HE DID SMITH IN THE FIRST MOVIE?


Chances are, he can’t.

There have been only five Ones before Neo.  They all probably acted differently upon 
gaining status of The One.  Neo experimented with his power in a unique way—by going 
inside Agent Smith.  The look on Neo’s face after Smith exploded indicated that he was
enjoying the power.  Neo probably wanted to see what it was like to be inside a 
program.

Anyway, as we all know, something happened and Smith became free.  The System realized
that whatever Neo did freed Smith—it must keep track of its agents.  Now, it would be 
bad enough to keep losing agents that way.  On top of that the System knows Smith is 
running around.  If Morpheus could see Smith during the Burly Brawl, the System must 
be able to detect him.  Since Smith figured out his powers between movies and probably
had to “come out” to do so, that’s when the System became aware of him and took 
precautions.  

Hence, the new agents are impervious to this particular move.  Neo realizes this as 
soon as he starts fighting them, muttering the “brilliant” one-liner “Hmmm….upgrades.”
Nothing left but to give them an old fashioned ass-whupping with plenty of eye candy.


WHY IS THE DANCE SCENE IN ZION SO LONG?


I’ve heard several people complain about this.  The dance scene is intended to give us
a feel of the Zionites, but that’s its secondary purpose.  Its main purpose is to
 supplement the Neo/Trinity love scene.

The love between Neo and Trinity is one of two factors that will once and for all 
break the System’s control (the other being Smith).   It’s why Neo chooses the other
 door later on.  What better way to express that love than through sex?  At least 
that’s what the Wachowski’s seemed to think.

Okay, so we’re going to watch Neo and Trinity have sex to show their love.  It would 
be a waste of screen time to watch the entire session (this is not a porno) so by 
intercutting with the erotic dance sequence we get sex in a specific and general 
thematic way.   We also get to pass time quickly, from the beginning to when Neo 
consummates and has the vision again.

*NOTE*  During consummation is when people usually feel the closest to the one they 
love, sexually.  It’s more dramatic to have Neo see the vision of Trinity dying at 
this point than ‘halfway through.’  This is why we have the lovemaking in its entirety
 and the dance scene to break up the passing of time.


HOW CAN SOMEONE BRING BACK A PACKAGE IF THE MATRIX ONLY USES THEIR MINDS?


I was thinking of this during the scene where Smith converts Bane.  The other guy, who
I think is named Malachi, returns with a package that is very important. I have been 
informed it is the Oracle's message to Neo on where to meet.  Makes sense to me.  
Bane's captian is Ballard who receives the message in ETM and later givesi t to Neo in
Zion.

Anyway, we know the rebels have their own constructs for training and leisure purpose.
It’s possible that when someone is carrying a package or other document/item of 
importance, that they are transferred to a safe construct upon leaving the Matrix.  
There, the captain may read it while in computer form.  

Or you can believe that the item is transferred to another electronic form, one that 
is readable in the real world.  
 

WHY IS THE MEROVINGIAN SO LONG-WINDED AND THE SCENE SO LONG?


This is similar to the Zion scene for storytelling purposes.  
The Merovingian discusses two important themes one can see throughout the movie:  
cause and effect, and the illusion of choice by those in power.  The latter is most
 prominently exemplified by Neo’s encounter with the Architect.

It would also be a flaw in the Merovingian’s character if he just gave up the 
Keymaker.  For the story and prophecy to progress, the Keymaker must be found by the
rebels.  So they could break into the Merovingian’s prison…if they knew where it was.

By introducing the dessert and the girl, the Wachowski’s are providing not only 
thematic discourse, but something else about the Merovingian—he cheats on his wife.  
This provides an alternate character with power of the Merovingian’s assets to help 
the rebels, but only as far as she wants.

Hence, the dinner establishes character of Persephone and the Merovingian and provides
themes and, more importantly, furthers the story by introducing interesting and 
non-compromising characters who may have another part to play.


WHY DOES THE KEYMAKER EVEN EXIST?  WHY NOT JUST SEND NEO TO THE SOURCE?


If you look at the plan outlined by the Keymaker as he knows it, it’s designed so only
the One can get to the source.  The rebels have no reason to believe he is lying—and
he isn’t.  He is only serving his purose.  The plan is geared to keep the rebels or 
any of the free programs from getting to the source.  The Keymaker will only outline 
the plan to the rebels, and as far as he knows only Neo can get in and see the 
Architect.  Wouldn’t be much of a control system if others were allowed.


WHAT HAPPENED TO NEO AT THE END OF RELOADED?


According to the Oracle from ETM, his mind got separated from his body and he is 
trapped between worlds.  Only Trinity can save him.  We’ll find out more next showing.


WHAT DOES SMITH WANT?


“Everything.”

“Purpose.”

There’s been a lot on this, so I’ll keep it brief.

Unlike humans, programs know what they’re purpose is at all times.  Watch Tron if The
Matrix isn’t good enuff.  When Neo joined with Smith, he disseminated, instead of 
destroying Smith.   One possibility is that the part of the Matrix that reads Neo as 
a human/free mind became copied onto Smith.  

So Smith suddenly found himself without a job, or a job he realized he didn’t like.  
After all, he “hated this place, this zoo” as he calls it in the first Matrix.  Like
everyone else with freedom, he asked himself what should he do with it?

Well, he has some powers gained from Neo, though working in a different way.  

Realizing he has this power, Smith found his purpose—“What do all men with power want?
More power.”—Oracle

Smith realized not only that he was outside the System, but that Neo was as well.  
Defeating Neo would not only be vengeance for the confusion he felt upon being free, 
but he hoped to access Neo’s power as the One for more control over the System and 
humans.

Basically, he wants power.


WHY WASN’T SERAPH IN THE FIRST MOVIE?  WHAT’S HIS ORIGIN AND PURPOSE?


To answer this fully, we must resort to ETM and the Smith/Bane incident.

Seraph guards the Oracle.  From what?  The answer is basically—Smith.

Smith was not a menace to the System in the first movie.  Whether you believe the 
Oracle is part of the system or not, Seraph was unnecessary in the 1st movie.  If the
Oracle can manipulate around the system, what does she need a guardian for?  But when 
an anomaly to both System and humans is introduced, a protector is required.

ETM tells us that Seraph believes his indebted to the Oracle.  This leads me to 
believe that she ‘freed’ him, or someone did.  If he was originally made to be her 
protector, then simple obedience would be enough to program into him.  My guess is he 
was a higher level of security for the System, considering his ‘backstage pass,’ or 
maybe the Oracle gave that to him.  Who knows.

The fact he leads her away just before Smith appears reinforces the above theory.


SO WHY DOES SERAPH FIGHT PEOPLE TO KNOW THEM?


Smith took over Bane then went into the real world.  Now, if Bane went back into the 
Matrix would his Residual Self Image ((RSI) look like Bane or Smith?  It’s possible 
that it would be Bane, most likely Smith, since that’s whose appearance we saw go over
the phoneline.  But the Oracle and Seraph most likely don’t know the extent of Smith’s
powers or how they work.  Seraph might believe that any rebel approaching him may be 
Smith in disguise.  Let’s face it—melee fighting is big in the Matrix, so it’s not 
unlikely Serpah can indeed tell by style whether someone is human or machine, also 
given his unknown origin.


WHY BOTHER WITH NEO TALKING TO THE COUNCILMAN?


The scene doesn’t seem to do much to further the story.  Though the Councilman claims 
not to have one, the Wachowskis’ have a point with this scene—after all, they left it 
in.

Well, let’s remember Reloaded is actually “half a movie.”  The characterization of the
Councilman may play up later in Reloaded.

The scene may also be the Wachowski’s way of driving a point—we indeed need machines
and they need us.  Filming it this way is their method of not hitting us over the 
head—too hard at least.

Why is this point important?  Well, the Oracle stated that she is interested in the 
future and that the only way to reach it was “together,” which implies an accordance
with machines and humans.  Humans rejected machines in the Second Renaissance and it 
became their undoing.  Machines are not being symbiotic with humans now, and we know 
the system will fall.  This theory implies a possible ending in which the machines and 
humans work mutually.   The fact that Smith is a common enemy of both may drive the 
two worlds together as well.