לפיכך אם עמד הנביא ועשה אותות ומופתים גדולים ובקש להכחיש נבואתו של משה רבינו אין שומעין לו ואנו יודעין בבאור שאותן האותות בלט וכשוף הן. לפי שנבואת משה רבינו אינה על פי האותות כדי שנערוך אותות זה לאותות זה. אלא בעינינו ראינוה ובאזנינו שמענוה כמו ששמע הוא. הא למה הדבר דומה לעדים שהעידו לאדם על דבר שראה בעיניו שאינו כמו שראה שאינו שומע להן אלא יודע בודאי שהן עדי שקר. לפיכך אמרה תורה שאם בא האות והמופת לא תשמע אל דברי הנביא ההוא. שהרי זה בא אליך באות ומופת להכחיש מה שראית בעיניך והואיל ואין אנו מאמינים במופת אלא מפני המצות שצונו משה היאך נקבל מאות זה שבא להכחיש נבואתו של משה שראינו וששמענו:
Therefore, if a prophet arises and performs great wonders and miracles and tries to contradict the prophecy of Moshe, our teacher, we do not listen to him and we know with certainty that those wonders [were performed with] trickery and magic. For, the prophecy of Moshe, our teacher, was not [based] on the signs [he performed] so we could compare this sign to another [prophet's] sign. Rather, we saw with our eyes and heard with our ears like [Moshe] heard. This [prophet that is giving a prophecy that contradicts Moshe's prophecy] is similar to witnesses that testify to a man concerning something that he saw with his own eyes, [but they claim to have] seen something different than what this man saw and different from what this man heard, therefore, this man knows with certainty that these are false witnesses. Therefore, the Torah says that if a false prophet comes with signs and wonders, you should not listen to his words, because this [false prophet] is bringing you signs and wonders to contradict something that you have seen with your own eyes. And since we only believe in wonders because of the commandments that Moshe commanded us, how can we accept this sign that is being brought to contradict the prophecy of Moshe that we saw and we heard?
The Rambam here bases this Mishna on a foundation of his philosophy. The Rambam believes that there is no such thing as an unnatural event that occurs in this world, except for those things that G-D built into creation to be unnatural. This is found in the Rambam's explanation on the Mishna in Avos (Perek 5) that speaks about the ten things that were created on the eve of Sabbath. Over there, the Rambam says that all miracles and wonders are within the realm of the natural.
With this in mind, we can understand his stance that a prophet producing a miracle proves nothing, because this miracle is within the realm of nature. However, the Torah, G-D and Moshe's prophecy are supernatural and thus, "untouchable" by any subsequent prophet. Every miracle is a natural phenomenon and thus can not be used to overrule something supernatural that is experienced with the senses. This is why we believe in miracles only because of Moshe's prophecy, because that is what brought the supernatural into this world. Without Moshe speaking to G-D and the Jewish people witnessing it, we would not believe that anything is supernatural.