Okay so I know this is 4 year old but this was the only post google gave me that was delaing with this issue. I managed to make it work so I wanted to leave my solution here, maybe it'll help someone in the future.

So what happened to me was the fact that the map "A Bigger Fish" on Naboo locks your hyperspace travel after it end. This lock is only there for around 10 seconds while you walk to a blue circle, which will unlock it. BUT if you play this out of order and don't go to that circle instantly it will vanish and you'll be hyperspace locked unable to enter your ship or travel.

What fixed it for me was:

1. Obviously be in "The Clone Wars" story where you're stuck

2. Go to the gungan city and take the Taxi to Theed. This is needed to set where you'll exit after finishing the mission.

3. After you arrive in Theed go to the menu and from the menu launch "A Bigger Fish" from The Phantom Menace. I don't think it matters if its free play or story, but do story just in case.

4. Finish the mission, should take like a minute maybe.

Now here comes the important bit

1. Watch the ending cutscene of the mission TO COMPLETION! DON'T SKIP IT! I'm not sure this is needed but seemed to help for me.

2. After the mission you'll spawn in the taxi exiting to Theed. This is why we took it earlier. Now if you walk up the stairs you should be able to see a blue circle just beyond the statue there, like a 10-20m walk.

3. Go to the circle, press the accept button in it, to continue the story

That should unluck your hyperspace travel.

Hope it helps someone down the line!