Later in the series, Lacus and Seigel Clyne (her father) was announced as traitors and spies by Patrick Zala because of an incident where Lacus gave Kira the Freedom Gundam. Basically ZAFT broke up into two Factions: the Zala Faction/ZAFT where people believed in Patrick Zala's ideal of wiping out the Naturals and creating a better world with just Coordinators. And the Clyne Faction where people believed in Lacus' ideal of peace where both Naturals and Coordinators can live peacefully together.

At first, Lacus used radios to promote her ideal with the help of a few ZAFT soldiers that worked (you can say) under-cover in the ZAFT military. Soon Lacus and Andrew Waltfeld stole Eternal, a transport ship that was specially made for transporting the Freedom and Justice Gundam along with the Meteor Units.

This was a whole new chapter for Lacus since now the Eternal will be entering the battlefield in order to promote peace between the people. But her ideals will remain the same and with the help of the/her people, she will continue to promote peace.