Since the show seems to be skipping back and forth between the Pirate Planet episode and the Chaos Pool I came to the following conclusion. Smokey is being portrayed as the Captain and as you can see how they both yearn for freedom.
Captain: This planet? This vile lumbering planet? Devil storms, Mr. Fibuli! You are a callow fool! Do you not see how my heart burns for the dangerous liberty of the skies? Plunder, battle and escape! My soul is imprisoned, bound to this ugly lump of blighted rock, beset by zombie Mentiads and interfering Doctors!
Mr. Fibuli: But what can they do to you Captain?
Captain: Enough! They shall die! By the flaming moons of hell, they shall die!
Whereas the Captain is bound to what he calls “This vile lumbering planet.” The MIB is bound to the island and has always yearned for freedom. The Captain also says his soul is imprisoned much the same way that the MIB’s soul or essences is trapped within the Smoke Monster. I also assume that the voice that we heard in “Jacob’s cabin” saying “help me” was the MIB because he was trapped or imprisoned.
I now fast forward to a scene to where the Doctor is in chains tied to a pillar by the Captain. The following conversation takes place after the Doctor riles the Captain up:
Doctor: You’re just trying to shut me up. You can’t kill me while I’m helpless.
Captain: Can’t I?
Doctor: No, you can’t. Because you’re a warrior and it’s against the warriors code. You should have thought of that before you tied me up.
Captain: By the hounds of hell.
Doctor: Hard to listen Captain when someone’s got a finger on a nerve, eh? What is it that you’re really up to? What do you want? You don’t want to take over the universe do you? No. You wouldn’t know what to do with it beyond shout at it.
[The Captain goes on to tell Mr. Fibuli to release the Doctor and he goes on to show/tell him part of his plan but not all]
I see this as summing up what the Smoke Monster is. Again I look back to Richard when he was chained up in the bottom of the ship. Smokey didn’t kill him almost the same way the Doctor summed up the Captain not killing him. When it came to others (i.e. Mr. Eko) however who were armed or a threat or not worthy as it were he was able to kill them. It was almost like a warrior’s code. When Richard was released the MIB went on to tell him part of what he thought he needed for him to hear in order to carry out his plan of killing Jacob but not the whole thing. The Captain then goes on and tells the Doctor the following:
Doctor: What are they for? [Referring to the mummified remains of the planets that he had plundered] Tombstones, memorials to the worlds you destroyed?
Captain: Not memorials, these are the remains of the worlds themselves.
Doctor: You come her to gloat at the wanton destruction you’ve wreaked on the universe.
Captain: [He whispers] I come here to dream of freedom.
I believe that this is where they got the idea for the MIB seeking freedom. The Captain himself yearns to be free. He has put together a plan to use the energy from the planets that he has gathered together to get inside the time dams that are keeping Queen Xanxia alive and thus kill her once and for all.
Fast Forward to the part near the end when Queen Xanxia shows her hand. The Doctor at this point has already figured out that the Captain was under the Queen’s thumb. She wanted eternal life and would do anything to get it. The Doctor and Roman stop their plans from making the Earth their next target and the Captain says the following when he finds Mr. Fibuli dead after the explosion on the bridge:
Captain: Mr. Fibuli… dead. Dead… He was a good man. Somehow, somehow Mr. Fibuli, my friend… you shall be avenged.
Queen Xanxia is killed shortly after that by Kimus.
Is this a sign of maybe what is to come? Will Zoe (By the way her name means life, ironic this is what Queen Xanxia wanted and that I think and have said in earlier posts that she is the Queen Xanxia of Lost) show her hand being a geophysicist may have figured out what the light is and is in search of it for herself. Will she be killed shortly after revealing what she is after much like Queen Xanxia? Then we come to the Captain kneeling over Mr. Fibuli. Could the “He was a good man” quote be a reference to Jacob? Will Jacob be killed and the MIB kneel over his body in much the same way. Remember the part where Jacob asked his mother “Am I good, mother.” Also I like that the Captain said “my friend” as that is one of the MIB’s signature sayings.
I then think the show will move on to the waterfall aka the “Chaos Pool” where the show will end with someone making a decision that will break the loop. I believe this to be Jack, because the one that made the decision at the Chaos Pool was the one who was shown to be someone else when they looked in the mirror. Which of our losties have been infatuated with mirrors the most? That would be Jack. But I do believe that Desmond will help guide him to the decision that he is going to have to make, the same way the Doctor did. I think that the decision made will end up sinking the island. Whether Jack eventually turns over the role of protector to Smokey/MIB/Locke and then he/it/they decide to sacrifice their existence in order to gain the only freedom that he/it/they can have… DEATH.
This is much the same logic that Xoanan the computer had: (Xoanan’s logic was destroy, be free). I once thought that we were going to come down to multiple personalities between the MIB and Jacob. Now I see that the multiple personality is going to be with Smokey/MIB/Locke and whoever else exists within the entity. Because of all the personalities “the protector of the island”, which I believe Smokey to be, is going to be shown to be somewhat insane like Xoanan the computer was. I do believe that you will get to see that when it is all said and done that the last words that are uttered by the he/it/they entity will be either free or freedom and quite possibly thank you. Everything from that point on in Doctor Who turned out fine as the universe was again set in balance. The Doctor ended up taking the key itself and jumping into the Chaos Pool and it turned it off as it were. Could Desmond the one who we know can survive the electromagnetic energy do something very similar?