Well ok a bit of a long reply but alas I have a lot to say *joking*...  (Yeah I know,,, I yap on a bit but what the heck it never
hurt anyone to make a long post :p well ok never hurts to much :pp)

Ok this is as far as I figure.  There are quite a few points to consider but the Halo story is slowly starting to make sense.

We know a few facts;

1- The monitor type droids such as Guilty Spark and that 2401 Penitent Tangent (the one the grave mind had) see humans as
reclaimers.  Particularly humans that have the index.  The Arbiter did have the index at some time though he was not referred to as
a reclaimer by the 2402 droid (monitor of station 05).  When the Brutes had the index they needed to have a human activate Halo.
The Brutes could not simply use the index themselves.

1a- Guilty Spark (and possibly the other monitors) seem to see humans as having activated Halo in the past.  They make several
references to past activities.

2- The Covenant have always hate humans since time remembered.  While the Covenant hate humans they have not attacked Earth.  It was
thought this was due to the Covenant not knowing where Earth was.  However the end of Halo 2 implies that the Prophets may have
known and even possibly protected Earth.

2a- A big question is why do the Covenant hate humans so much. I think it is possible that the Covenent were also present when Halo
was last activated.  Possibly some Covenant (likely including elites and Prophets) were in the Ark at the time.  The Covenant might
not have wanted humans to activate Halo.  However Halo was activated and initially the Covenant would have hated humans for
destroying almost all sentiant life except that which survived on the ark (possibly Earth).  Eventually over time the entire story
was forgotten but the Covenant knew of humans as creatures to be despised.  This also begs the question of if some of the Covenant
knowing the location of Earth.  It is likely that many forgot the location over time.  However some Prophets may have still
remembered as they would have access to many records that common Covenant do not (and possibly the Prophets hid this knowledge).

3- There was one surviving Forerunner ship located within the city/base of High Charity.  This is possibly the Forerunner ship that
the original surviving Covenant used to leave the Ark.  As time went on the true nature was forgotten and this vessell was merely
seen as a holy icon.  In fact the ship became the very center of the Covenant life.  Being the primary source of power and possibly
knowledge.

3a- When the Prophets learn that the index is found and activation of Halo is imminent they try to use the Forerunners ship in the
hope of getting to the Ark.  The oracle tells us that the Ark is a place outside the kill zone of the Halo rings.  The Profit of
Truth is the only Prophet to make it to the ship.  The Master Chief makes on board as well.  The ship travels to Earth.  This
implies that the Ark is either on Earth and/or more likely is Earth itself.  There would need to be a control room but it is likely
that the entire Earth is the Ark.  Hence a place where life can begin again after a Halo activation.

4- Meanwhile the Flood now control what is left of High Charity.  With the Forerunner ship being removed High Charity has lost its
primary hyperdrive engine and power source.  However there is a Hyperdrive on board the Ember Clad that has been left on High
Charity.  Will the flood use the hyper drive technology to travel around?

4a- Cortana has been left on board High Charity.  We see a final scene where the Gravemind is about to question Cortana.  Will she
spill the beans and tell all allowing the flood to reach Earth?  Alternatively will Cortana overload Ember Clad's reactors?  At the
moment she would prefer not to do this as it would destroy herself and she is hoping the Master Chief will return for her.

4b- (Personal Opion).  The gravemind is very curious about what is happening.  It has possibly survived since the last activation
hence knows that the Halo's true purpose may not be to eliminate the flood.  I think there is something more to the fact that the
flood have the ability to live beyond death than meets the eye.  Maybe the forerunners were tampering with eternal life and messed
something up.  Hence creating their own demise.

5-The Covenant is now split.  Some races (such as the elite, grunts and hunters) have gone against other races such as the Brutes,
Buggers and Jackals.  Due to the assistance given by Sargeant Johnson, Mirandah Keys and the Arbiter the Elites may ally with humans
in the future.

6- (more opinion) How did Sargeant Johnson get off Halo before it was destroyed.  Well that is a good question.  Hmmmm.  I think he
found a way to use that teleportation system to transfer himself to either another ship or, more likely, Earth.  However how he
would get the energy required to do this is anyones guess.  Possibly he used some of the nergy from the blast or simply used the
last remaining energy in one big jolt.  Remember the Monitor made it to another Halo without any problem.  So it is possible there
is a Teleportation system capable of long range jumps. Who knows.  ***Shrug***

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Anyway that is about the jist of it all.  I hope it at least makes half sense *grin*.  There is a lot of things happening in the
game and it will be interesting to see how it all unfolds.  Anyway it seems we will have to wait a while for Halo 3 as it is not
expected to come out before the release of the PS3 (not to long away, but not to short either :p).

As for the Halo movie well it seems it will happen eventually.  Apparently Bungie and what not are making deals with Hollywood
pretty much as we speak.  The main concern is not to make just another Hollywood version of some sci-fi movie that is only pumped
out to make money.  The real issue is to actually make a good movie that is true to the Halo universe and style.

Well I hope you are having a good holiday :)

Well here you go this is how Seargant Johnson survived (I just found this now).

http://en.wikipedia.org/wiki/Halo_characters#Sergeant_Johnson

Basically he got on board a Pelikan and was able to survive in some Halo debri until he was piccked up by the Master Chief and
Cortana.