You can load a scene without destroying anything in the current scene with SceneManager.LoadScene with LoadSceneMode.Additive.
Example: SceneManager.LoadScene ("SceneName", LoadSceneMode.Additive);
That way all the objects from the loaded scene get added to your current scene. Both scenes now coexist with each other.
Note that all scripts from the "background scene" are still active, so you might want to set your input controller to inactive while the minigame is active.