The Winona Dakota Unity Alliance (WDUA) began its history in 2003-04 in response to the Grand Excursion 04 (GE04), the 150th anniversary of the original Grand Excursion, under the direction of President Millard Fillmore. The original excursion was a flotilla of paddle wheel steamships celebrating the opening of the upper Mississippi to large boat traffic, providing travelers opportunities to see the newly acquired western lands opening for development. Cities visited by the original flotilla along the upper Mississippi were encouraged to plan celebratory events for visiting passengers and communities. The City of Winona organized a GE04 committee to plan the local events. In the planning process, it became apparent that the American Indians of the upper Mississippi and the impact of the original Grand Excursion on their histories and daily lives had not been included in the celebration. The Winona committee wanted to recognize formally and include the Dakota people who had inhabited the area before the opening of the west.

A new subcommittee was formed which became the future basis of the WDUA. Tribal representatives and subcommittee members met in Winona and on Dakota reservations to plan an event of reconciliation and homecoming. The result of the planning was the 1st Great Dakota Gathering and Homecoming, June 2004, shortly before the arrival of the flotilla.

Subcommittee members (now the WDUA) realized that truth and reconciliation were essential in order for the communities to come together. Education of the public about the history and culture of the Dakota people was vital as well. They recognized that this was a chance for the Dakota and the community of Winona to work together in understanding our commonalities, differences, and the true history from several perspectives while forging a new future. They also recognized the gravity and importance of what they were undertaking. The only blueprints for such an activity that were available were the South African model of truth and reconciliation procedures and the wacipi (powwow) organizational structure. This new committee worked with Dakota tribal and spiritual leaders as guides through the process. As a result, the 1st Gathering had the following components held at Lake Park, Winona:

1. A Saturday public truth and reconciliation forum attended by local, state, and federal representatives, clergy from Roman Catholic and Protestant churches, and Dakota and Winona community members.
2. A Sunday ecumenical service including Dakota and Winona clergy and music groups from Minneapolis.
3. Wacipi (powwow) with a Grand Entry on each day.
4. Moccasin Tournament
5. Four community meals
6. American Indian vendors
7. Professional American Indian singers and musicians

The City of Winona and major financial contributors helped to launch the 1st Great Dakota Gathering and Homecoming. Community volunteers staffed the event.

The success of the event encouraged the subcommittee to formalize its functioning as a 501(c)3 non-profit organization, the Winona Dakota Unity Alliance in time to work with the City of Winona in planning the 2nd Gathering held in June 2005. Since then, the WDUA with the generous support from the City of Winona, businesses, other non-profits, and individuals, has organized gathering events each year for a total of thirteen events. Community members have responded with enthusiasm in the forms of volunteering and attending activities.