Like his father's before him, his was a stormy career; indeed, he had to face a fiercer tempest than even the one in the sound of which he had been reared. It was the question of the government of the college which brought about the first clash, and out of this developed the great battle known as the ‘Battle of the Two Constitutions’ (1879-85), which resulted in the growth of personal antagonism between him and some of the leading men of his denomination. He insisted that the government of the college should be in the hands of the subscribers, whereas his opponents maintained that the governing body should consist of representatives appointed by the churches in each county. The leader of the opposition was John Thomas of Liverpool (1821-1892) (q.v.) who, according to M. D. Jones, wanted to ‘presbyterianize’ the denomination. The quarrel spread to the churches, and the whole country was thrown into a turmoil. The party which supported M. D. Jones was called the party of the ‘Old Constitution’ and the other the party of the ‘New Constitution’ (sc. of Bala Independent College). The position deteriorated still further owing to the prominent part played by M. D. Jones in the movement to establish a Welsh colony in Patagonia; he was driven to this partly by the spirit of nationalism, and partly by the radicalism bred in him on account of the oppression of the Tory landlords in Wales. However, he lost a considerable sum of money in this enterprise and, because of straitened circumstances, was forced to sell Bodiwan (his home and the seat of the college) to the college committee in order to meet the calls upon him; this, too, was held against him. The opposition succeeded in getting the ‘New Constitution’ passed, but he refused to recognize it, and at a committee held at Shrewsbury (1879) — ‘The Decapitation Committee,’ as his partisans called it — he was dismissed. For some time after this the Independents had two colleges at Bala, one under M. D. Jones at Bodiwan and the other, which belonged to the ‘New Constitution’ at Plas-yn-dre. This was in charge of Thomas Lewis (1837-1892) (q.v.), and was transferred to Bangor in 1886. In the end, both colleges were re-united, but M. D. Jones was permitted to remain at Bala in charge of the department of first-year students; this, however, did not imply that he had budged an inch from his original position. He resigned in 1892 in order to facilitate the arrangement whereby there, should be a single college at Bangor, to be known as ‘the Bala-Bangor College.’

He was a born fighter and could not bear opposition. He was also an out-and-out nationalist, the father of the nationalist renaissance in Wales; he loathed the English-worshipping Welshman, and it has been said that ‘the credit should be given chiefly to him and to Emrys ap Iwan (q.v.) for transforming Welsh patriotism into a vigorous practical nationalism.’ He d. 2 Dec. 1898 and was buried in the Old Chapel burial ground at Llanuwchllyn.