It originally started as an alliance between the San'Shyuum (Prophets ... members of the former Covenant who looked for asylum on Earth. Later conflicts over the Halo rings and Forerunner tech ...
This marks the beginning of the end of the UNSC-Covenant war ... and regains the Prophets' trust. All this happens in the opening hours of Halo 2, which is a good example of how much more ...