public static void main(String[] args) {
    String tempString = "";
    String tempStringTwo = "";
    String [] convertedLines = new String [100];
    int counter = 0;
    int tempcount = 0;

    File file = new File("input.txt");
    if (!file.exists()) {
        System.out.println(args[0] + " does not exist.");
    return;
    }
    if (!(file.isFile() && file.canRead())) {
        System.out.println(file.getName() + " cannot be read from.");
    return;
    }
    try {
        FileInputStream fis = new FileInputStream(file);
        char current;

        while (fis.available() > 0) { // Filesystem still available to read bytes from file
            current = (char) fis.read();
            tempString = tempString + current;
            int character = (int) current;
            if (character==13) { // found a line break in the file, need to ignore it.
                //tempString = tempString.replace("n"," ").replace("r"," ");
                tempString = tempString.replaceAll("\r|\n", " ");
                //tempString = tempString.substring(0,tempString.length()-1);
                //System.out.println(tempString);
            }
            if (character==46) { // found a period
                //System.out.println("Found a period.");
                convertedLines[counter] = tempString;
                tempString = "";
                counter++;
                tempcount = counter;
            }

        }
    } catch (IOException e) {
        e.printStackTrace();
    }
    System.out.println("------------------------------------------------");
    for (int z=0;z<tempcount;z++){
        System.out.println(convertedLines[z]);
    }
}


Here's my current output...
------------------------------------------------
The quick brown fox
jumps over the lazy dogs.
Now is the  time for all good men to come to the
aid of their country.
All your base are
belong to us.

Here's what I need...
-----------------------------------------------------
The quick brown fox jumps over the lazy dogs.
Now is the time for all good men to come to the aid of their country.
All your base are belong to us.