There are some route served by the airline and the stops between Jakarta and Jayapura:
- Jakarta (CGK) - Surabaya (SUB) - Makassar/Ujung Pandang (UPG) - Sorong (SOQ) - Manokwari (MKW) - Sentani Jayapura (DJJ)
- Jakarta (CGK) - Makassar/Ujung Pandang (UPG) - Biak (BIK) - Sentani Jayapura (DJJ)
- Jakarta (CGK) - Denpasar (DPS) - Timika (TIM) - Jayapura (DJJ)
- Jakarta (CGK) - Makassar/Ujung Pandang (UPG) - Sentani Jayapura (DJJ)
Personally, I hate take-off and landing, because most airline required us to go to the terminal when the airplane stop even with same aircraft. Garuda Indonesia is one that give passengers option to leave to terminal or stay on the airplane on transit when the next flight is use the same aircraft. But, transit is still annoying me, because I can't sleep well during landing because seat have to be upright.
The good news, Lion Air now serve direct nonstop flight from Jakarta to Jayapura using JT-794 depart from Jakarta (CGK) at 22.30 GMT+7 and arrive at Jayapura (DJJ) at 06.00 GMT+9 (5 hours 30 minutes). My last flight using Lion Air was good. I slept few minutes after take-off and awake near arrival at Sentani Jayapura (DJJ). This is good for people who hate take-off and landing.