Sure! Here's a sample of a simplified ninja game using HTML, JavaScript, and CSS. This is a text-based game as creating a fully visual, graphical game with good gameplay and graphics would require extensive resources and is beyond the scope of a simple response. However, you can still play and navigate through the game by typing commands. The game incorporates some of the requested features such as fighting rogue ninjas, unlocking skills, exploring, and checking stats.
To play the game, simply copy and paste the above code into an HTML file and open it in a web browser on your smartphone or computer. Once the game starts, you'll be prompted to enter your ninja name. The game will then guide you through the missions, fights, skill unlocks, exploration, and eventually, the boss fight. The game will display alerts to provide you with updates and feedback.