This is easily the finest episode of any TV series I've seen. Everything is brilliantly done and seamlessly integrated from the start.
We have jeffster overdubbing a brilliant action set piece, a plane full of commandos, Sarah looking the most stunning she's ever been and enough moments to make you cry. Oh, and kung fu.
In every episode they seem to pick just the right music. In this episode they truly excelled.
If you want a happy Chuck ending, leave it at this as subsequent seasons just cannot match.
One thing that doesn't work plot wise is the chuck /Sarah relationship. At the end of last episode they kissed and finished holding hands. At the same time Sarah wanted to go on the run with Chuck. Now we're at least a day later and seemingly they never spent the night together, and the next morning Sarah is off to a new mission in a different country. Makes no sense at all. The story changes, of course, but at that moment things were set.