O'Neill was, like many Gaelic Irish officers in the Spanish service, very hostile to the English Protestant presence in Ireland. In 1627, he was involved in petitioning the Spanish monarchy to invade Ireland using the Irish Spanish regiments. O'Neill proposed that Ireland be made a republic under Spanish protection to avoid in-fighting between Irish Catholic landed families over which of them would provide a prince or king of Ireland. This plot came to nothing. However in 1642, O'Neill returned to Ireland with 300 veterans to aid the Irish Rebellion of 1641.
In the nineteenth century, O'Neill was celebrated by the Irish nationalist revolutionaries, the Young Irelanders, who saw O'Neill as an Irish patriot.
Owen Roe O'Neill was serving as a military adviser to Don Fernando in the Netherlands at the time of the Ring of Fire. O'Neill's future history as an Irish nationalist was discovered after Don Fernando obtained history books from Grantville, which he provided to O'Neill. O'Neill still bore animosity towards England, even when it was part of the League of Ostend.
He later played a key role in extracting Luke Wadding from Rome, and in rescuing Frank and Giovanna Stone from the Castell de Bellver. O'Neill and other Irish Geese soldiers were made Pope Urban's bodyguards to replace the slain Swiss Guards.