Did you prompt the user for the story (1)? I didn't see the first double underscored word prompted (2).

package com.teamtreehouse;

import java.io.IOException;

public class Main {

    public static void main(String[] args) {

        Prompter prompter = new Prompter();
        String story = prompter.newPrompt();
        Template tmpl = new Template(story);
        prompter.run(tmpl);

    }
}

package com.teamtreehouse;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;


public class Prompter {
    private BufferedReader mReader;
    private Set<String> mCensoredWords;

    public Prompter() {
        mReader = new BufferedReader(new InputStreamReader(System.in));
        loadCensoredWords();
    }


    private void loadCensoredWords() {
        mCensoredWords = new HashSet<String>();
        Path file = Paths.get("resources", "censored_words.txt");
        List<String> words = null;
        try {
            words = Files.readAllLines(file);
        } catch (IOException ex) {
            System.out.println("Could not load censored words");
            ex.printStackTrace();
        }
        mCensoredWords.addAll(words);
    }


    public void run(Template tmpl) {
        List<String> results = null;
        try {
          results = promptForWords(tmpl);
        } catch (Exception ex) {
          System.out.println("There was a problem");
          ex.printStackTrace();
          System.exit(0);
        }
        String render = tmpl.render(results);
        System.out.printf("Your TreeStory: %n%n%s", render);
    }


    public String newPrompt() {
        System.out.println("Please enter your story, with blanks as descriptive words such as 'name' or 'adjective' surrounded by '__' .\n\n");
        BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
        String readLine = "";
        try {
            readLine = mReader.readLine();
        } catch (IOException ex) {
            System.out.printf("Problem getting input. %s\n", ex.getMessage());
        }
        return readLine;
    }

    public List<String> promptForWords(Template tmpl) throws IOException {

        List<String> words = new ArrayList<String>();
        for (String phrase : tmpl.getPlaceHolders()) {
            String word = promptForWord(phrase);
            words.add(word);
        }
        return words;
    }


    public String promptForWord(String phrase) throws IOException {

        String word = mReader.readLine();

        while (mCensoredWords.contains(word)) {
            System.out.printf("%s is censored. Try again. ", word);
            word = mReader.readLine();
        }
        return word;
    }
}