I’ll start this off by saying, I’m not suggesting that this will happen in Halo 4, but rather that it could happen at some point in the series future.
Towards the end of the Human-Covenant War, there were approximately 20 million San 'Shyuum, most of which were located on High Charity. When the Flood reached the Holy City, they were almost completely wiped out. According to the Halo 3 Bestiarum, this left less than 1000 San 'Shyuum. More recent information suggests that even more have died and the rest have vanished, likely going into hiding. With there small numbers, there’s little possibility the the remaining San 'Shyuum could do much for now.
But when we look at what little we know of the San 'Shyuum’s history, a few more possibilities are found. Just over 4500 years before the events of the games, the San 'Shyuum had a bloody civil war. Long before this time, a Forerunner Dreadnought crash landed on the San 'Shyuum’s home planet. The San 'Shyuum revered Forerunner technology and believed that was a sacred artifact and should not be interfered with. Eventually a group, known as Reformers, voiced there desires to enter the ship and learn from its technology. This sparked the war between the Reformers, and the Stoics (those who believed that tampering with or directly studying Forerunner artifacts was blasphemous and heretical). Eventually the Reformers made it into the Dreadnought and took flight from the planet, breaking off a massive chunk of rock in doing so. This piece of rock would later become the foundation of High Charity. The Stoics were left behind.
Although the Reformers had achieved victory and left the Stoics (who sent out communication messages threatening that they would be -Yoink!- for their impudence toward the gods) behind, they realized that they were doomed due to the small number that had joined their cause to control the Dreadnought. With an extremely small gene pool, they enacted strict controls around mating to prevent potentially disastrous inbreeding, an act that had to continue until their demise.
It was the Reformers who fought against the Sangheili and started the Covenant. It has been said that the star orbited by the San 'Shyuum’s homeworld went nova, destroying the planet along with everyone on it, such as the Stoics. However, it has also been suggested that the San 'Shyuum lied to the other species of the Covenant and their home planet is still very much inhabitable. The reasons they would lie are many but if this is the case it holds many possibilities. The Stoics could make a return. Chances are they wouldn’t be too pleased with the humans or the former Covenant species, all of whom have tampered with Forerunner technology.
That said, they are certainly not the ancient enemy. In fact, the San 'Shyuum are ancient allies of humanity. Perhaps this will also come in to play.