Remember way back in season 3 when the others had Kate and Sawyer helping to build a runway?! This was a few days after the sky turned purple and the Others lost communications with the mainland. Ben said once the submarine left the island, it wouldn't be able to come back, but Ben ALWAYS has a plan. They were going to use Ajira as their new transportation but then Jack and Co. had to go and make the call to the frieghter, putting on hold anything to do with Ajira
Fast Forward
The island is shifting through time and the losties find themselves on the beach where their camp is, but with no one around, only vincent's leash, the canoes, and the Ajira Airways bottle. When the island moved into that time, I believe it was in a period after the oceanic six came back. The canoes were just there as if people rowed them into the island...and the Alcatraz island is the only place they could've come from. So the oceanic 6 used Ajira to get to the alcatraz island, then they used the canoes to circle around the island until they reach their camp, upon finding it empty the losties split up and search only to come back to find one of the canoes missing. Not knowing who stole their canoes, they chase after them shooting, not knowing it's really their friends Theory by Batmanman
Fast Forward
The island is shifting through time and the losties find themselves on the beach where their camp is, but with no one around, only vincent's leash, the canoes, and the Ajira Airways bottle. When the island moved into that time, I believe it was in a period after the oceanic six came back. The canoes were just there as if people rowed them into the island...and the Alcatraz island is the only place they could've come from. So the oceanic 6 used Ajira to get to the alcatraz island, then they used the canoes to circle around the island until they reach their camp, upon finding it empty the losties split up and search only to come back to find one of the canoes missing. Not knowing who stole their canoes, they chase after them shooting, not knowing it's really their friends Theory by Batmanman
