O’Donnell represented a newer generation of nationalist politicians. He became national secretary of the UIL, and remained loyal to William O’Brien even after O’Brien’s resignation from the IPP in 1903, trying to orchestrate his return to the party. When land agitation flared up in 1905 he was imprisoned for his part in it to two months hard labour.
He was re-elected in the January 1906 general election despite attempts by south Mayo priests to oppose him, squashed by O'Brien's threat to abandon a pact with the party to avoid contests at the election. After the election O’Donnell was identified as one of the little knot of O’Brien’s die-hard supporters, both he and D. D. Sheehan being expelled that autumn from the IPP. In 1908 O’Donnell formally rejoined the party on the initiative of its leader John Redmond, in the interest of unity. In the January 1910 general elections O’Donnell was returned for O’Brien's newly founded All-for-Ireland League, this time through clerical support against an anti-clerical opponent.
However in the subsequent December 1910 general elections he was forced to retire through lack of support, while an Irish Party boycott drove his newspaper out of business in 1911. He retained links with O’Brien but never made a political comeback.