What does this phase mean. The 'end' of a story where all the threads are tied up?

It means the last part of a story. "Threads" are the parts of a story that you've told, such as the main story with the conflict and climax, along with all of the sub-plots that have been happening around the main story. "Tying them up" just means that everything that's happened in your story gets explained, and the reader has a satisfied feeling at the end of your story instead of wondering what just happened.