(disclaimer - You would be dumb to read this if you aren’t caught up )

As we are nearing the end of the fourth season of this incredibly awesome show, there are still so many aspects that need to be answered. From the smoke monster in season 1, to time travel in season 4, the questions that need to be answered keep piling up. So here is a list of some plot points with some questions on each one that need to be explained. 

Big Toe Statue

I still haven’t been able to forget about this after Sayid, Jin, and Sun discover this while sail-boating the end of season 2.

Where did this come from?
When was this built?
Why does it only have four toes and why is the rest of the statue missing?
Is the statue of the ‘god’ of the island?

The Smoke Monster

It has killed people (Echo was awesome) on the island, and remains one of the biggest puzzles on the show.

Why does it make that clicking noise like an adding machine?
Does it involve magnets in any way?
Can Jacob control or use the Smoke Monster?
Why did the Smoke Monster not kill John Locke in season 1?
How does Roses’s comment on the sound of the monster being familiar to her and on being from the Bronx work into play?
Does the monster produce visions from one’s past?

Jacob

This bad boy is the ruler of The Others. They all seem to fear him, including Ben. Ben has stated that Jacob can cure cancer,which may explain how Rose is now healthy.

How come he was invisible to Locke during the encounter in the cabin?
Why did Jacob tell Locke “Help Me”?
When Hurley discovered the cabin, why was Jack’s father in there?
How does the cabin mysteriously move and vanish into thin air? 
How can Jacob know all the mysteries of the island as Ben claims he can?
Why is Jacob so interested in Walt?

The Numbers

Although bits and pieces have been released on the numbers, they have yet to be explained. Yet, they appear all over the show. Hurley hears them being spouted from a crazy in the psyche ward, and wins the lottery using them, which leads him to believe he is cursed. Danielle Rosseau hears a transmission and follows it, which causes her to crash her boat on the island. On a map, the coordinates are near Kosrae, an island of Micronesia. They were printed on the side of the swan hatch in which Hurley noticed, as Lock blew the hatch at the end of season 1.

But who is responsible for the numbers?
How do they involve the island?
Why do they appear almost everywhere?
Why were ‘these’ numbers so important that they had to be repeatedly entered in a computer?
What is so special about them?

Walt

He must be pretty damn important if Jacob told Ben to put him on the list. Yet, we have not seen him since the end of season 2. But there is no doubt that he has some sort of powers. Remember when Michael told Walt he’d go look for Vincent as soon as it stopped raining, and it immediately stopped? When Walt grew angry that someone wasn’t paying attention to him while reading a book on birds, and suddenly a bird just slammed into the window and died? Ben was also notified about Walt’s strange behavior after his capture, and was pointed towards a few dead birds. Walt’s stepfather was actually scared of him and didn’t want Walt. Walt set fire to the raft near the end of season 1. Numerous characters have claimed him as special or different, including Locke.

How did Walt know of the Hatch when he warned Locke not to open it?
Why is Walt appearing in other people’s visions and why did he appear to prevent John Locke from killing himself?
How did Walt get his powers and where the hell is he?
How did Walt communicate to Michael through the computer?
Why is Jacob interested in him?

The Disease and Vaccine

Desmond injected himself with a vaccine for 3 years to prevent himself from getting sick. But we also see a rip in Kelvin’s suit when he goes outside. Ben does talk about it after he is captured. Rousseau strongly believes in this disease, as her entire crew got sick and died shortly after reaching the black rock. Also, when Claire was abducted, Ethan injected her with a vaccine, the same one Desmond used on himself. But Juliet told Jack that the vaccines were used to save Claire’s life and the baby. We also know now though that Claire is not in the picture (in the present).

Is the disease just a hoax?
Does this disease only effect pregnant woman, or is that just part of what it does?
How come no one has been infected on the show yet or is that what Minkowski died of on the freighter?
Did the virus kill Claire?
Does the disease only effect people that can travel in time?

The Island

A good amount of the characters on the island were brought to it by accident. There may be meaning behind this as well as the miracle of this many people surviving a horrible plane crash.

Where exactly is the island located and how come it is so hard to find?
What time effect delay (31 minutes) does the island have compared to the rest of the world? 
Why does leaving the island have side effects (Desmond in the helicopter) if you don’t stay on the exact coordinates (as explained by Farady)?
Does the island only help those who serve a purpose and is that why Locke temporarily lost the use of his legs, which ended up getting Boone killed?
Why are random objects from different periods of time stranded on random parts of the island (the ship Black Rock, airplanes, etc.) ?
How did the Dharma initiative find it?
Why is Charles Widmore interested in the island, and why does Ben claim he wants to ‘exploit it’?

Ben Linus

He is one of the most interesting characters on the show, and we don’t entirely know if he is good or bad. He is masterfully manipulative, and there are more questions surrounding him than anyone else. Sayid discovered his secret room with numerous passports and currency, so we know Ben has access off the island. Miles has stated they are looking to find Ben Linus and shows a picture of him taken at an airport. And sometime in the future, Sayid is assassinating people for Ben.

Can Ben time travel?
How does he have access to have such massive sums of money (Miles asks for 3.2 million)?
Why does he so fiercely want to protect the island?
Why is Sayid killing people for Ben and who else is on Ben’s list?
How is he as powerful as he is?

The Mystery behind Through the Looking Glass

In this season 3 finale shocker, a troubled and drug addicted Jack attends a funeral of Jo[.. ..]antham, which he finds in a newspaper on an airplane.We learn that Jack and Kate are both off the island, and that Jack desperately wants to go back. John Locke could be in the coffin, as he did hate his father, and could go by a different last name. When Jack asks Kate about going to the mystery person’s funeral, she responds with a disgusted ‘Why Would I go to the funeral?’ This makes it clear that Kate hates this person. No one attended the funeral besides Jack, so this person has no friends or family.

Who is in the coffin?
Why is Jack so messed up he nearly kills himself?
why does he ‘have to go back to the island’?
How did Jack and Kate get off the island?
why is Jack sick of lying, and what is he lying about?
Why does he yell ‘Get my father down here’ at the hospital?
And a few other specific questions that still have me perplexed:

How does Jack end up so far in the forest after the crash? 

Why was Jack’s Dad’s coffin empty?

What was the reason Hurley was in the mental institution in the first place?

What happened to Desmond after he turned the key?

How come Richard has not aged, he is the same age now as when he met Ben as a kid?

Why won’t Jack see Aaron?