A: 101 actually appears a number of times in all three films, and though no one knows exactly what it means (if anything), the popular explanation is this: 101 is binary for 5 (which to a computer is the sixth number because computers count from 0), and the events of the three films take place in the 6th interation of the Matrix. Neo is the sixth One, this is the sixth time the machines have destroyed Zion, etc. We learn that this is the sixth iteration from The Architect's conversation.
Another popular explanation for its prominence: 101 is a direct reference to George Orwell's 1984. Room 101 is the place in which a persons greatest fear of all is enclosed. Thanks to Daniel Bryan-Curnow for the Orwell reference!

A: For some pieces, it isn't completely obvious where they fit in, but here's the order we're pretty sure of:

1. The Second Renaissance Parts I & II
2. A Detective Story
3. The Matrix
4. Kid's Story
5. Final Flight of the Osiris
6. Enter The Matrix
6.5. The Matrix Reloaded
7. The Matrix Revolutions
8. The Matrix Online

There's quite a bit of time between 1 & 2, 5 leads directly into 6, and 6 and 6.5 run parallel and weave in and out of each other's plots with 6 starting just before 6.5. The other Animatrix episodes are less clear: Program, World Record, and Beyond could all happen anytime between 2 and 7. Matriculated feels different, it could probably be placed around the time of 4 - 6.5, but there's no way to tell for sure. Of course, some of these Animatrix episodes may very well happen during previous versions of the Matrix itself, but that's another story :-).

A: We goofed on this one. A number of you (Joseph Guendert being the first) wrote in to remind us that the machines have destroyed Zion five times already (see answers further down if you don't know what I'm talking about), so duh, they have to know where Zion is. Taking it a step further, the machines actually set Zion up each time with help from the One, so they pick the location in the first place.

A: The Animatrix episode, Final Flight of the Osiris, details this. Basically, the hovercraft Osiris comes upon the giant digging operation and realizes that Zion is located directly below the drills.

A: With 6 months between the first movie and Reloaded, there's a lot of time for something bad to happen. His sister Zee says "I lost two brothers to that ship", so it seems reasonable to conclude that Tank wasn't as 'ok' as he thought and he simply succumbed to his injuries from Cypher's attack. All we know for sure is that he definitely died between the two movies.

A: Link is married to Zee, Tank and Dozer's sister. Considering her brothers' untimely and violent end prior to Reloaded, Zee is understandably nervous of Link serving aboard the Neb under Morpheus.

A: The Animatrix short, Kid's Story, gives his background. Neo contacts him because he's a candidate to be freed, much as Trinity contacted Neo. After this contact and a lengthy Agent chase, Kid is able to self-substantiate himself into the 'real world' and considers Neo responsible for this.

A: Niobe used to be with Morpheus, and is now with Commander Lock. Lock doesn't believe the prophecy and mistrusts Morpheus. Niobe is caught between the two, but seems more sympathetic to Morpheus' beliefs and supports him (instead of Lock) at key moments in Reloaded.

A: This is quite a controversial scene amongst fans. Our interpretation is that this primal dance scene is meant to hammer home the differences between Us and Them - between humans and machines. Humanity is all about dirt, sweat, emotion, sexuality - machines are emotionless, antiseptic, incapable of celebration, hope, or love. The scene reminds us of how high the stakes are before the impending war. If the machines win, something palpable will be lost, something that can't be simulated by the machines. The scene also offers a break before we hurl headlong into a brutal war.

A: Bane is a crewmember on another hovercraft - otherwise unremarkable until Agent Smith takes him over in the Matrix, immediately before Bane jacks out. Bane now appears to be Smith in the 'real world', with the same motivations as Agent Smith, like destroying Neo.

A: These are "backdoors" in the Matrix. Programmers create a "backdoor" to allow a secret way into a system, often undetectable by the system administrators. This hallway of "backdoors" is also invisible to operators on hovercrafts: it doesn't show up on their green code screens.

A: It's unclear what the reason is, but Seraph definitely has a purpose. Has the Oracle been targeted by the machines? She's not in her apartment baking cookies anymore; she's moving, hiding behind "backdoors" in the system, so a protector (firewall) makes sense, but it's never explicitly revealed what she's hiding from.

A: She's telling him it isn't about choice. He's made the choice and now he has to understand the choice and its ramifications. So, what's the choice? I think it's Trinity. To love, share, and ultimately save her. To have that bond with another person will greatly influence future actions of the One, especially in the scene with The Architect.

A: The Keymaker has the key to the Source. He's the only one who can get Neo where he needs to go to destroy the Matrix. The Oracle explains his importance and sends Neo to find him.

A: They're mirror images of each other. Neo dies and is resurrected. Smith "dies" and is resurrected. Upon resurrection, they each possess greater control over their abilities, and a greater sense of purpose. Is the connection specifically because Neo flew into Smith to destroy him, or is there something else going on?

A: It's Rama-Kandra and his wife, Kamala. They're the parents of Sati, all three of whom are more prominently featured in Revolutions.

A: Causality. Action and reaction. For him, it's not about the choice, it's about the reasons for it. Not far from what the Oracle is talking about, but it seems like all this is a game to him, while the Oracle certainly takes it more seriously. Merovingian is challenging this One (and he's definitely experienced some of the other Ones - so does he always have the Keymaker? Have all the Ones had to go through this same trial on their way to the Source?). He's challenging Neo to understand his motivations, probably with an eye to poking holes in those motivations. I think Merovingian has a crucial role to play in the overall trilogy - I think we'll see more of him in Revolutions.

A: Persephone appears to be an "emotional vampire". The kiss downloads the subject's emotions. What value this has to Persephone is anyone's guess. Also, the kiss may be a temptation, a distraction, to make Neo stray from the path, like the Sirens in Homer's Odyssey.

A: The Architect is the creator of the Matrix. If there is a God figure for this reality, the Architect is it. His conversation with Neo is critical to understanding what follows, and also what has come before. See the Meaning section for a more thorough explanation, but here are the basics: Neo is the sixth One. Zion (the free world) is another form of control to house those whose bodies/minds reject the Matrix. The prophecy is a load of bunk. The One is meant to find the Source and The Architect, leading to the destruction of the current Zion, and select a number of people to start over as the whole thing is reloaded and Zion is built up from nothing all over again. Basically, the machines control the free minds in the 'real world' as much as the captive minds in the Matrix.

A: There's no evidence indicating these are the previous Ones, or for that matter, that the previous Ones look like Neo. They're more likely showing all of Neo's possible responses or the machine's predictions of his responses.

A: All the other inhabitants of the Matrix that we've met so far (Agents, Seraph, The Oracle, etc) may be programs, but they interact regularly with humans. They need to be able to communicate with normal people on a regular basis, and their programming reflects that in the way they speak. The Architect is a machine that never has to communicate directly with humans, therefore he tends to talk like a machine would when talking with other machines. He uses big words, overly complicated sentences, and purely logical expressions of his message - not exactly the way people talk to each other.

A: For appearances. If it was too easy, or the Agents weren't viciously effective, someone in Zion would get suspicious. Additionally, Kevin Stokker pointed out that the machines need some control over the rate of minds-being-set-free. He proposes that if it's too fast, the humans may be harder to control; if it's too slow, Zion may not be able to muster the strength/infrastructure necessary to cultivate, train, and propel The One into the Architect Chamber with the impunity that they need to in order to complete another cycle. I like it. Thanks, Kevin!

A: Trinity. Previous Ones were motivated by the same love of life, of humanity as Neo, but Neo's love is more clearly focused on Trinity rather than the whole human race. Previous Ones picked the door to save Zion (which does happen in a sense - current Zion inhabitants die in this scenario, but Zion is reloaded, so it lives on), but Neo picks the door back to Trinity and saves her. This is a fundamentally different choice, and is unexpected by the Architect. This will lead to a different outcome than the previous five times this has happened. For more, see Meaning.

A: It's likely that picking the wrong door wouldn't immediately cause the crash, but it would set in motion a chain of events that would cause the crash: Zion wouldn't be given up, The One's code wouldn't get assimilated, the Matrix wouldn't get reloaded, and the One would prolong the battle, all contributing to the catastrophic failure that would soon follow.

A: He's the One! Neo's expanded capabilities in the Matrix not only allow him to see it differently than anyone else, it also allows him to manipulate it on a greater level than anyone who's come before. In this case, Trinity is plugged in to the matrix. Therefore her brain is part of and accessible to the Matrix. Neo actually went into and joined her mind instructing her brain to pump her heart bringing her back to life. Remember she was not really mortally wounded. Her brain only thought she was and Neo instructed it otherwise. This was visualized by watching Neo cup his hand around Trinity's heart and gently squeeze it. [Thanks to Michael Packer for the assist!]

A: Another noodle-baker. Some believe the 'real world' is just another level of the Matrix. A Matrix-within-a-Matrix, or just another manifestation of the same thing. Therefore, Neo can manipulate it the same way as any other part of the Matrix, he's just never tried. I don't buy that theory. I think Neo was changed by experiencing the Architect firsthand, and then by picking Trinity's door. No one's done that before, and all bets are off now. Things are not going according to the expected script, and I think this experience changes Neo. For more, see Meaning.

A: It's Bane/Smith. He's tried to stab Neo, he's likely responsible for the destruction of the resistance ships near the end of Reloaded, he's the only survivor of that debacle, and he's in the bed next to a comatose Neo. Not good. Not good at all.

A: They all appear on The Architect's monitors as flashbacks from Neo's life.