You can use this expression when:

• There's a bad situation.
• It seems like the situation is going to get better, BUT...
• Something else bad happens.

For example,

Just as you started to think we were finally headed toward an economic recovery, unemployment goes up again.

You can always use it in the opposite situation, when it seems like something bad is going to happen, but then you get saved:

Just as I started to think that we were lost, Samantha found the trail again.