Fairfax and Major General Skippon spent most of April 1645 at Windsor superintending the assembly and training of the army which was to prove the decisive factor in the war but which the royalists spoke of contemptuously as the “New Noddle,” while the King himself referred to Fairfax as the Parliament’s “new brutish general.” Even the Scottish allies of Parliament had doubts and Robert Baillie, writing to a friend in the United Provinces, said : “This new-modelled army consists, for the most part, of new unexperienced soldiers; few of the officers are thought capable of their places.” Before the army had reached its full strength it was needed in the West. The royalists had laid siege to Taunton and Fairfax was despatched to the aid of Robert Blake who was defending the town. Setting out from Windsor on 30 April with some 11,000 men and passing through Newbury, Andover and Salisbury, Fairfax reached Blandford in Dorset on 7 May. Here he received orders from the Committee of both Kingdoms to return, but to send a detachment to the relief of Taunton. Accordingly a brigade, consisting of four regiments of foot and five regiments of horse under Colonels Welden and Graves, was sent off and its arrival forced the royalists to abandon the siege of Taunton. Meanwhile Fairfax had marched back and passing through Ringwood, Romsey, Alresford and Whitchurch reached Newbury again on 14th. He was next ordered to besiege Oxford and sending for the artillery left at Windsor he marched into Oxfordshire.

While Fairfax was besieging Oxford, events occurred which jolted the cumbersome machinery of the Committee of both Kingdoms. In Scotland the Marquis of Montrose, on behalf of the King, captured Dundee and defeated a superior force under Hurry at Auldearn, while in England the King himself with Prince Rupert assaulted and captured Leicester. With the royalists at Leicester it seemed that the counties of the Eastern Association were in danger and Fairfax was ordered to abandon the siege of Oxford and to march against the King. The Committee of both Kingdoms removed all restrictions on his authority and made him dependent, not as hitherto on the Committee, but only on the advice of the officers of his own Council of War.