Here's my take. I keep seeing a lot of the same questions, so hopefully this explanation can answer a lot of them.

For the purposes of analysis, I'm going to assume that the plane level is actually reality, whether or not that's true. If everything's a dream, then there are really no rules, and anything is possible.

Secondly, I'm also going to assume that limbo is a state of consciousness, not a specific dream level. Limbo is simply the place you go when you lose track of the fact that you're dreaming. It could therefore be assumed that "normal" dreams are limbo states, albeit far less powerful ones than the ones depicted in shared dreams. It is relatively simple to escape from limbo: you just have to die. However, this is a much more terrifying prospect in limbo because, by its very nature, limbo means that you believe you are dying "for real." Think of the "waiting for a train" scene: neither Dom nor Mal was completely sure that their world wasn't reality, so it was very hard for them to lie down on those tracks.

Chronology:
Reality: Everyone is on the plane to LA, connected.
Level 1: City streets. Yusuf stays awake as everyone else descends into level 2. Everyone else is connected to each other. Saito is dying.
Level 2: Hotel. Arthur stays awake as everyone else descends into level 3. Everyone else is connected to each other.
Level 3: Mountain fortress. Eames and Saito stay awake. Fischer is shot and descends into level 4 (which is limbo for him, because he cannot tell that it's a dream). Dom and Ariadne connect to Fischer and descend into level 4.
Level 4: Dom's world. Dom uses his old dreamworld to house Fischer's subconscious.
Level 1: Meanwhile, Saito dies in level 1. He is not connected to Fischer/Dom/Ariadne in Level 4, so he enters his own, separate limbo state. It could be considered "level 4b."
Level 4: Ariadne tosses Fischer off the balcony. He dies, sending him back up to level 3, where...
Level 3: ...his subconscious arrives just in time to fill his newly resuscitated body.
Level 4: The weather goes nuts and Ariadne throws herself to the wind as...
Level 3: ...the building collapses, kicking her back.
Level 4: Dom vacillates about staying in the limbo state with Mal. Presumably, he does ultimately escape, probably by dying. He does not, however, ride the kick back to level 3 with Ariadne.
Level 3: Just as the building's exploding...
Level 2: The elevator explodes upward, kicking Fischer, Ariadne, and Eames back to level 2. Simultaneously...
Level 1: The van hits the water, kicking Eames, Fischer, Ariadne, and Arthur back to level 1. Eames becomes Browning once again so he can go see whether the inception took. Ariadne and Arthur are distressed because Dom does not wake up. Dom drowns in level 1, where he is still connected to Saito. Therefore, when he finally escapes from level 4, he enters Saito's limbo state with him.
Level 4b: Dom is unsure of whether he's in reality, but somehow he can instinctively find his way in the limbo state, possibly because he's been in a similar situation before. He must convince Saito (and himself) to commit suicide. Presumably he is successful, because...
Reality: The drug wears off. Everyone, including Saito and Dom, wakes up, alive and well.

I think that covers just about all of the major questions and "plot holes."

1 more question, how did Cobb so sure that Mal will kidnap Fischer, and how did she do that?

Err..A question here. When fischer and ariadne fall off the balcony in level 4, why do they end up in 3?? U see a kick has to come from an earlier dream. So to wake up from level 4 the kick has to be done in level 3. And cob himself said that dieing in the dream would send them to a limbo where they would be trapped forever. So Fischer and ariadne didn't die in level 4 but they didn't experience any kick either.

At this point I am beginning to question the use of destroying the fortress. Was it used as a kick to wake up from a higher level??
The fortress exploded in level 3 so that means it was meant to be a kick for a higher level i.e level 4. So that means that ariadne and fischer make the transition from 4 to 3 because of the destruction of the fortress. But then why the hell did fischer and ariadne jump off the roof. What purpose did it serve??

So if all they had to do was kill themselves while in Cobb's limbo to get out of it, what was the point of Earnes blowing up the complex and thus inducing the kick for the limbo?

waveking wrote:Err..A question here. When fischer and ariadne fall off the balcony in level 4, why do they end up in 3?? U see a kick has to come from an earlier dream. So to wake up from level 4 the kick has to be done in level 3. And cob himself said that dieing in the dream would send them to a limbo where they would be trapped forever. So Fischer and ariadne didn't die in level 4 but they didn't experience any kick either.

only if the dreamer was heavily sedated, that he will be send into limbo when he died in the dream world, Yusuf also explained why they need such big movements to successfully performed a kick (it suppress all senses except the sense of balance)

so i can only assume that when Ariadne and Cobb connect with Fischer to rescue him, they were not under the heavy sedatives

Dan_87 wrote:1 more question, how did Cobb so sure that Mal will kidnap Fischer, and how did she do that?

Mal is his guilty subconscious, so she always tries to sabotage him (i.e. he always tries to sabotage himself because he is so guilty about planting the idea in Mal that lead to her reality confusion). His deduction that Mal would kidnap Fischer represents nothing more than his knowledge of himself. He knows that his subconscious will attempt to prevent him from succeeding. And I suspect it would have been successful, had it not been for Ariadne's help.

waveking wrote:Err..A question here. When fischer and ariadne fall off the balcony in level 4, why do they end up in 3?? U see a kick has to come from an earlier dream. So to wake up from level 4 the kick has to be done in level 3. And cob himself said that dieing in the dream would send them to a limbo where they would be trapped forever. So Fischer and ariadne didn't die in level 4 but they didn't experience any kick either.

Fischer was in limbo, so, as per my theory, he could escape from limbo (back to level 3) by dying. Ariadne was simply in a deeper level of the dream, so she's kicked back by the snow fortress's collapse.

waveking wrote:At this point I am beginning to question the use of destroying the fortress. Was it used as a kick to wake up from a higher level??
The fortress exploded in level 3 so that means it was meant to be a kick for a higher level i.e level 4. So that means that ariadne and fischer make the transition from 4 to 3 because of the destruction of the fortress. But then why the hell did fischer and ariadne jump off the roof. What purpose did it serve??

Exactly. It seems that the kick was useless, because it was how fast they committed suicide that they returned to level 3. Cobb didn't make it in time for the sequenced kicks because he didn't die until his limbo actually collapsed onto itself, and was thus transported over to Saito's limbo.

MrFang wrote:
Fischer was in limbo, so, as per my theory, he could escape from limbo (back to level 3) by dying. Ariadne was simply in a deeper level of the dream, so she's kicked back by the snow fortress's collapse.

So if the kick was meant for only Ariadne and Cobb, why did she try to kill herself? And in turn, why did she make it back through all of the synchronized kicks while Cobb didn't?

Yeah, I think you are pretty spot on with this. While watching the movie, I spent a lot of time just trying to keep track of the rules of the dream world, and what I've gleaned (though it may be completely wrong) is that what occurs in each level of the dream directly impacts the level that directly proceeds it, which explains why the tumbling van affected the hotel level but not the snow level etc. This rule applies in the opposite direction as well, which is why a separate kick was required in each level; the kicks acted as a cascade or domino effect, with each kick affecting the preceding level. A seemingly obvious point to make, I know, but I have seen some questions on here about it so I thought I would throw in my two cents. Also, I think you are right about Ariadne and Cobb being linked to Fischer in limbo as a result of direct "hooking up", but what I had theorized before reading this was that because it was Cobb's subconscious that killed Fischer, Cobb's subconscious world engulfed Fischer, which resulted in Fischer's limbo taking the form of Cobb's world. Cobb then entered this incarnation of limbo and convinced this self-made world to "release" Fischer, which caused him to re-enter the 3rd level. As for the end, I wanted the spinning top to result in the ambiguity of the entire movie, but upon further exploration I think that it only brings the reality of the occurrences after limbo into question. Earlier in the movie the audience was shown that at least up until the plane, Cobb was in reality because we were able to see Cobb's totem perform its purpose (we viewed it fall in at least one circumstance). I think that the ambiguity of the ending only refers to the question as to whether Cobb and Saito actually escaped Limbo or not. Again, I could be totally wrong, but thanks for reading.