everything that happened on the ISLAND happened
the ATL (alternative timeline) didnt exist as we know it, there was no time frame.
when they died at certain points they all ended up there, only when jack died they made their way to the church and connected. that was the bit many people couldnt get their head around, it was quite clever. the last scene with jack walking through the jungle then dying was epic
still think it was a bit of a cop out though, mind you that was the only way they could keep the majority happy i guess.
as has the rest of humanity that originally got excited about this utter load of carp.
each to their own, IMO one of the best shows on TV in years as it wasn't spoon fed to you like other crap, you had to think for yourself and it caused much discussion, it was original.