Scotland was formally re-united to England by an Ordinance of the Commonwealth Parliament dated 12th April, 1654, and the cross of St Andrew was ordered to be brought once more into conjunction with that of St George:
And that this Union may take its more full effect and intent Be it further ordained by the Authority aforesaid That the Arms of Scotland viz: a Cross commonly called Saint Andrews Cross be received into and borne from henceforth in the Arms of this Commonwealth as a Badge of this Union.
In the new great seal which was prepared in 1655 the St Andrew's cross was quartered with St George's cross and the Irish harp, but it was not at once introduced into the naval flags, although placed on the obverse of naval medals struck in 1654.
The cross of St Andrew was re-introduced into the naval flags by the following order of the Council of State dated 18th May, 1658[182]:
That the Standard for the Generall of his Highness ffleete be altered, and doe beare the Armes of England, Scotland, and Ireland, with his Highness Escutcheon of pretence, according to the impression of the Great Seale of England; and that the Jack fflaggs for the fflagg officers of the ffleete and for the severall Shipps of Warre of his Highness be the Armes of England and Scotland united, according to the auncient forme, With the addition of the Harpe, according to a Modell now showd; and that the Comrs of the Admty and Navy to take order That the standard and Jacke fflaggs be prepared accordingly.
In the standard the two crosses and the harp were borne "quarterly" surmounted by an inescutcheon (sable, a lion rampant argent), the personal arms of Cromwell[183], but in the other Admirals' flags and the jack the crosses were superposed, as in the Union flag of 1606, with the addition of a harp in the centre. The "model" has disappeared, like all its predecessors, and nothing remains to show for certain whether this harp was placed in a blue escutcheon as in the earlier Commonwealth flags or not, but since a request was received from Chatham in the following November for 200 yards of blue bewper "for ye altering of all ye fflaggs and Jacks here yt are of ye former fashion into ye new forme[184]" it seems on the whole probable that the harp was in an escutcheon with a blue field.
This return towards the flag of 1606, prophetic of the coming restoration, lasted for a few months only. In September Cromwell died, and his son, the shadow of a great name, after being tolerated as a mere figurehead for a few months, was in the following May forced to abdicate. The remnant of the Long Parliament, which had just re-assembled, passed an "Act for the Great Seal of England" which restored the seal of 1651 with its map of England and Ireland and shields with the St George's cross and the Irish harp. The cross of Scotland vanished and the Commonwealth "Cross and Harp" jack supplanted Cromwell's Union Jack.
In March, 1660, the Navy Commissioners were told to furnish General Mountagu, then in command of the Fleet [185], "with Standards for the Naseby suitable to the Jacks now worne in the ffleete[186]." This was the standard which Mountagu was flying when ordered to cross to the Hague and bring back the king.
On 1st May, 1660, the newly assembled Houses of Parliament passed a joint vote for the restoration of the ancient government, and a few days later, before Charles was publicly proclaimed, the Commissioners of the Admiralty and Navy, at the instance of the Council of State, issued the following order to their subordinate Board: