Allow me to clarify some things. The Covenant’s return is covered in the novels Glasslands and The Thursday War. Jul ‘Mdama, a Sangheili who we see in Spartan Ops, is a radical who joins a terrorist organisation called the Servants of Abiding Truth, they still believe in the Great Journey and their goal is to stage a coup against the Arbiter and attain power over their home planet to rebuild resources. Ultimately, they desire to wipe out humanity once and for all because they believe that humanity will also recover and expand across the galaxy. Jul is captured by ONI during an arms deal between Avu Med ‘Telcam (leader of the Servants) and an ONI team assigned to supplying the terrorists with weapons so the Elites can wage a war of attrition against one-another with neither side emerging victorious. Jul is transported to a Forerunner Shield World that humanity has taken over called Onyx, but the events of the novel Ghosts of Onyx lead humanity to call it Trevelyan due to the sacrifice of a Spartan-II to ensure his team made it inside the Micro Dyson Sphere. While in-captivity, Jul plots his escape, as the scientist in charge of the facility assigns him a Huragok (Engineer) named Prone to Drift to lead him around various Forerunner sites inside Trevelyan. To make sure Jul doesn’t try to escape, an explosive harness is placed over him. Over time, Jul learns from Prone about a Forerunner called the Didact, an ancient warrior who waged a war against humanity 110,000 years ago and was sealed away at a planet called Requiem. Jul gradually grows to understand the Forerunner language, and eventually discovers a way to escape captivity when he stumbles upon a dmaged portal system. Threatening to detonate the harness, he persuades Prone to take it off, and he takes a leap of faith into one of the damaged portals. Jul ends up on a distant colony world called Kelekos. It’s inhabited by a remnant of the Covenant who haven’t been seen since the early days of the war, they’re absolutely fanatical in their beliefs and see Jul as their new prophet sent to them - as they believe that the Didact is a holy warrior who will come to save them when he’s released. Jul is appointed as their leader, he manages to re-establish contact with Sanghelios and learns from his friend that his wife, Raia ‘Mdama, has been killed by the humans, as the Arbiter requested Lord Hood to use the UNSC Infinity’s MAC gun on Sanghelios to wipe out a Brute uprising and the attack of the Servants of Abiding Truth. Jul’s hatred towards humanity becomes personal, he gathers his new Covenant army at Kelekos and discovers a portal to Requiem - reactivating it with his ability to read Forerunner glyphs, and setting out to awaken the Didact. Thus, the ‘Storm Covenant’ is born. It should be noted that the 'Storm Covenant' isn't a majority of the Sangheili race, many remained loyal to Thel and Earth is apparently protecting "too many Covenant asylum seekers". Not all goes to waste, we're only seeing one side of this branching conflict, there was no way that [i]every[/i] Elite was just going to frolic in grassy fields with humanity after 30 years of spearheading a genocidal war. This also raises one of the more interesting themes of Halo - whether to judge a species by an individual, a group, or their actions as a whole. You seem to have generalised the Elites as a whole based on the actions of a group, but I suspect that's because we're given a very one-sided story in the game.