Lost, like its spiritual predecessors Twin Peaks and The X-Files, was built on a series of interlocking mysteries. When the curtain fell on Season 6 earlier this year, many of the questions had been answered. Some satisfactorily, some not. However, the majority of fans weren't so upset by the answers they got. It was the questions that the writers left hanging which caused the real anger.

Season 6's DVD exclusive epilogue, New Man In Charge answers a few questions (if rather sarcastically) by having Ben carefully explain things to pair of dim-witted DHARMA employees who have been faithful to the Initiative for years, and claim that they "deserve answers" for their devotion. The subtext there is not especially difficult to read. If you wanted to know where the food drops were coming from, why there was a bird that could say Hurley's name, or indeed, if you still hadn't pieced together where the polar bear came from, this DVD extra will give you what you want.

But, for most of us, the unsolved mysteries were bigger than those, all which could be pieced together from implications within the show itself. We didn't need to see a DHARMA station on the mainland responsible for sending food out on automated drones to figure out what was going on, and knowing doesn't make anything about the show much clearer. There are questions left which muddy the waters of Lost, and with the show definitively over, it's hard not to find that a bit maddening.

So, Den Of Geek has picked out the five biggest mysteries that we think Lost never satisfactorily answered, and we'd like to hear your theories. Any comments about polar bears will, of course, be entirely ignored.

5. Who was the other Christian Shephard?

In all fairness, it was made clear in the show that the majority of Christian Shephard's appearances were actually Smokey, who existed in Christian's form between the first episode and the point where he assumed the form of Locke. Unfortunately, there are a number of appearances which don't match up with this: the moment where Christian appears to Michael on the Kahana, the moment where he appears to Jack in Los Angeles, the moment where he appears to Sun and Frank while in the form of Locke elsewhere.

These appearances are categorically not the Smoke Monster, particularly the two which occur off the island. Maybe you can stretch Jack's LA vision to a drink/stress-induced hallucination. Maybe you can stretch Michael's to a stress-hallucination too (even if it would make no sense for him to hallucinate Jack's father). But you can't reasonably suggest that Smokey chose his conversation with Sun and Frank as the one moment where he decided to be in two places at once.

So who was the ‘other' Christian Shephard? The ghost of the original? And if so, why did he care what was going on with the island? As much as I want to believe that the Lost writers had it all planned out, things like this make the Smokey/Christian connection feel like a square peg, round hole situation, one answer chosen of several options, despite the fact it didn't fit perfectly. Please, give us more credit.

4. The Sickness

After years of hinting, Season 6 finally showed us what 'The Sickness' was. As far as answers go, it was far from being the clearest. Indeed, to this day, it's not really clear whether it was Rousseau or her crewmates who had the sickness, and indeed, whether the sickness (as she understood it) existed at all.

We do know that Sayid's sickness was real. We just don't know what it was. As shown, it appears that the sickness infects people who are brought back from the dead in the Temple, but only when the waters do not run clear. There are some tests which can be done to determine whether someone is ‘sick', but it was never explained how (or even if) they work. And despite knowing all that, we never really saw what the sickness was. We just saw Sayid becoming a bit emo-goth, but eventually realising he wasn't actually all that bad.

So, a shiny virtual penny to anyone who can explain what the wider context of the sickness was, how many people we know were infected (besides Sayid) and why Rousseau was so afraid of it. It appears to be one of the few components of the Lost mythos that doesn't actually fit anywhere in the plot. It was simply a property of the island which occasionally got referenced and that the writers apparently wanted to address. In a way, it would have been easier to reconcile it if they hadn't bothered.

3. Jacob & Co?

I was a big fan of the episode, Across The Sea, which told the story of Jacob, his brother, their mother (and adoptive mother) and those living on the island at the same time. But even I can't deny that, in a general sense, the knowledge we gained in that episode didn't really explain the mythos so much as bump it up a level. It's a logical trap even a child can recognise.

Admittedly, I would argue that the origin of these characters isn't so important , but what they do is. Their adoptive mother, who some have speculated may have been a smoke monster herself, clearly knew more than most, since she identified the source and the consequences of tampering with it. But where did this knowledge come from? Did someone choose her? And if so, who chose them?

Ultimately, knowing Jacob's history doesn't expand on anything much except Jacob. Fair enough, Lost always did focus on the characters, but we need to know either why Jacob and company were special, or, if they weren't, why they mattered more than those before them.

2. The Rules

The moment at the end of Season 4's ninth episode, The Shape Of Things To Come, was a big one. Ben Linus broke into Charles Widmore's bedroom and calmly explain that, by allowing mercenaries to come to the island and kill Alex, he had "broken the rules" and would be punished. It looked as though we were getting a major new puzzle to solve.

Indeed, further references cropped up. Jacob and Smokey would often discuss how ‘the rules' prevented them from interfering with one another directly. When Dogen told Sayid to stab Smoke-Locke under a specific set of circumstances, it appeared to be because such an act was governed by the rules. In fact, Smokey's attempt to find a loophole in the rules was arguably the motivating factor for almost everything that went on in Lost.

And what did we get to explain these rules to us? Not a lot. Allusions. References. Allusions to references. The pointed appearance of board games, governed by rules, and various people claiming that things were either inside or outside the rules which existed.

But did anyone scratch the surface of the bigger questions: what are these rules, who imposed them, and why must they be followed? No. No, they didn't. In fact, Lost made its entire audience aware that Smokey breaking the rules and escaping the island would be the worst possible consequence for everyone, but we never really found out why he was bound by them in the first place.

1. The Numbers

When the numbers first cropped up in Lost's eighteenth episode, Numbers, they were an exciting addition to the series, one that seemed poised to form an integral part of the mythos. By Season 2, they were dominating the show's landscape, and had captured the imagination of the fandom, all of whom were waiting for the truth about what they were and what the big mystery about them was. Expectations were high. Really high.

So, perhaps that's why many rank the failure of the show to provide a reasonable explanation as one of the biggest flaws. Sure, there's the ‘official' explanation (as revealed in the semi-canonical "Lost Experience") about the Valenzetti Equation, but that explanation never appeared in the series. There's also the revelation that each number corresponded to a candidate for Jacob's position, but that list was, after all, just a list. Jacob admitted as much to Kate.

It's hard to say what went wrong. Perhaps they were never intended to become as big a focus as they were. Perhaps the ‘real' explanation was junked when the writers saw how high expectations had become. Maybe they were just making it up as they went and simply couldn't come up with a good explanation as to what caused the strange properties of the numbers. Either way, there's simply no other contender for the top position on this list. Of all the mysteries Lost failed to tie up satisfyingly, this is the one that'll frustrate people long, long into the future.

Which unsolved elements have left you mystified or miffed? Seek answers and offer possibilities in the comments...

See also:

• The 10 best Lost episodes