I recently read that the current Sanhedrin went to the mikveh and then ONTO the Har Habais. My question is as follows: I remember learning that the reason why we can go onto the Har habais is because we are Tamey Met. If this is the case a mikveh won’t help because you need the ashes of the Para Aduma. If so how can the Sanhedrin have gone onto the Har Habait?

The rabbis who forbid going onto Har Habayit did not check the issue thoroughly, they made their decree out of doubt. It's what's called forbidding out of "policy", not out of "Torah", since that is ot the practice in other unclear cases. Even if such a decree would have been done according to Halachic rules, it would need an assembly of all the Gedolim of the generation, or the Sanhedrin. Then the majority would need to decide on forbidding the ascent to Har Habayit. Since it wasn't done, the Halacha remains, as it always has been, that ascending to Har Habayit is permitted, as the Rambam did, and the Meiri too said the common practice was to go on to Har Habayit. What's more, every Gzera which cancels a Mitzva (such as Ketroet, or Korban Pesach etc.), even indirectly, needs to have a set time, and we have never heard of a specific time for this Issur. Some wish to do a Syag, and keep people from doing an Issur, but on the other hand, it causes many who do go onto the mountain, to go not as Halacha specifies. It is Halacha that Tamey Met is allowed on the Har in some places - "Machane Levia" (Rambam Biat Hamikdash 3:4), and since there are places where we know for sure that they are Machane Levia, one who may want to go on to Har Habait in purity, after Tevila to wash Tumat Keri, and under the requirements of Mora Mikdash (and, of course, knowing the path permitted for Tmeim, which one should not stray from), has a big Mitzva. Regarding the Sanhedrin going onto the Har - The Sanhedrin did not go institutionally, only the Semuchim who think it is permitted went. The Sanhedrim as an establishment is dealing with the questions of the borders of Machane Levia and it will take some time until they give a Psak on these issues. Rabbi Yishai Babad