The Ancient Covenants, referred to in Rassilon's Guide to the Multiverse, volume 3 as the Great and Ancient Covenant, were the "very laws of the continuum," forged in Event One, which governed and bound the Transcendental beings and protected the Six-Fold-Realm. The Sixth Doctor described the ancient laws and covenants that prevented the universe from becoming a "blood bath" as the "insensate authority" of the Lux Aeterna, citing it as the reason a war between the primal forces had never occurred.
Although we and the Transcendental Beings share the time vortex, the Covenant divides us. But the Six-Fold Realm is denied us by the Covenant, and it is the Covenant that we dare not transgress.
According to the Covenants, fulfillment was forbidden for Eternals. Additionally, the four dimensions of space-time were forbidden to the Chronovores. They were unable to leave their twin domains of Calabi-Yau Space and the time vortex unless summoned by a being in the "Higher Place" opening a path for them. Once a link was forged between the two regions, be they spatial, temporal, dimensional, or otherwise, the Chronovores were free to pass between them. The Sixth Doctor stated that not even the Guardians of Time could prevent this.
When Elektra and Prometheus conceived Kronos, the Guardians dealt with their violation of the Covenants by unraveling Prometheus's existence. Lillith, Elektra's mother, considered the child an abomination, anathema to the Ancient Covenants, and wanted it destroyed. But the Guardians imprisoned it instead and cast it into the vortex.
When the war council of survivors of the Millennium War agreed to forget the conflict ever happened, the God of the People called out to the Guardians, demanding fulfillment of the Ancient Covenants. The Guardians appeared, and used the Key to Time to erase the memory of the War.
After the Sixth Doctor helped Kronos to defeat the Mad Mind of Bophemeral, the Chronovore Lillith and Eternal Sadok appeared inside the TARDIS and, owing him a favour, offered to reverse the Doctor's accidental destruction of Maradnias, asking "Remember the Ancient Covenant that we send down to you?" The Doctor told them to do what they thought was right, and time was changed so that him and Melanie Bush had never visited the planet. (PROSE: The Quantum Archangel)
The Seventh Doctor explained that the Celestial Toymaker could occasionally step outside of his sliver of reality but that he couldn't fully leave it, and this was a result of the rules set down for him in the childhood of the universe. (AUDIO: The Magic Mousetrap)