The pilot reported that on departure from Coconut Island when he retracted the gear he heard an abnormal clunk. The gear unlocked light extinguished, but the pilot noticed that the aircraft was 10 knots slower in cruise indicating that the gear doors were not fully closed. On arrival at Horn Island the gear was selected down and there was no down indication for the left main gear. The pilot recycled the gear twice, changed gear indicator globes, tried sideslipping, and followed all procedures set out in the Emergency Checklist for failure of the main gear. A 500 ft flight over the airport and inspection from the ground confirmed all three wheels were extended but it could not be confirmed if they were locked. The pilot commenced an approach to runway 08 after emergency services were in place. After touchdown the left gear collapsed, and the aircraft came to rest off the left side of the runway but within the flight strip. The left gear retraction rod had failed during gear retraction at Coconut Island.