I did "Trouble on the Homefront", ended up killing the overseer and leaving Amata in charge. Then told to leave the vault.

Now, I have zero quests, and seems there is no end to the game now.

How do I end the story ?

Trouble on the Homefront is not part of the main plot. It's a side quest. If it was available to you, that means you've finished The Waters of Life main quest. The next one is Picking up the Trail which should start right after Doctor Li talks to Elder Lyons in front of the Citadel. If it didn't start, it means you most likely encountered a bug.

I finished "Picking Up the Trail" and the related story arc that ends with "Who Dares Wins"

Then I went to Vault 101 to follow up on the distress call I got during "Who Dares Wins"

Then the game is over. Who Dares Wins from the Broken Steel DLC finishes the whole main plot of Fallout 3. There's nothing more. You can freely roam the wasteland, finish any remaining side quests and explore locations you've missed. Trouble on the Homefront is a side quest from the base game, so it's strange that you've came across it so late.

Every single quests is complete after getting banished from Vault 101.

There is no ending now, or atleast that seems to be the case.

What do you mean by every single quest is completed after being banished from Vault 101? The only one that should finish is Trouble on the Homefront. If the game has finished any other quests automatically, this means that you've encountered a bug.

As for the second part, you won't get anything more than the ending after Who Dares Wins. A more satisfactory ending you've already encountered. It was after Take it Back! (or Project Impurity if you've chosen the bad version), but that was before the DLC. With Broken Steel add-on the game doesn't have an ending in meaning of credits followed by a transition to the main menu. You can play how long you want. This is intended for people who just want to freely explore the game after finishing the main plot.