The complete news of his displacement and supersession in rank does not appear to have reached him before this. His efforts to secure the restoration of his rank proving useless, he applied for immediate sea duty. The next attempt on the part of the Marine Committee to gratify Jones's wish for active service, and avail themselves of his ability at the same time, took the shape of a resolution of Congress authorizing him to choose the best of three ships which it was proposed to purchase in Boston, which he was to command until some better provision could be made for him. He was ordered to that point to fit out the ship. During this period of harassing anxiety he gave great attention to formulating plans and making suggestions looking to a more effective organization of the new naval establishment Window Type Air-Conditioner.

To Robert Morris, chairman of the committee, on different occasions, he communicated his views on this important subject in a series of valuable letters, of which the following are pertinent extracts:

"As the regulations of the navy are of the utmost consequence, you will not think me presumptuous, if, with the utmost diffidence, I venture to communicate to you such hints as, in my judgment, will promote its honor and good government. I could heartily wish that every commissioned officer were to be previously examined; for, to my certain knowledge, there are persons who have already crept into commission without abilities or fit qualifications; I am myself far from desiring to be excused. From experience in ours, as well as from my former intimacy with many officers of note in the British navy, I am convinced that the parity of rank between sea and land or marine officers is of more consequence to the harmony of the sea service than has generally been imagined... I propose not our enemies as an example for our general imitation; yet, as their navy is the best regulated of any in the world, we must, in some degree, imitate them, and aim at such further improvement as may one day make ours vie with and exceed theirs 100w box mod."

With regard to the difficulty of recruiting seamen, some of whom, finding the merchant service or coasting trade was broken up, had entered the army at the beginning of the war, while many more had engaged in privateering--a much more profitable vocation than the regular service--he says:

"It is to the least degree distressing to contemplate the state and establishment of our navy. The common class of mankind are actuated by no nobler principle than that of self-interest; this, and this alone, determines all adventurers in privateers--the owners, as well as those whom they employ. And while this is the case, unless the private emolument of individuals in our navy is made superior to that in privateers, it can never become respectable, it will never become formidable. And without a respectable navy--alas! America. In the present critical situation of affairs human wisdom can suggest no more than one infallible expedient: enlist the seamen during pleasure, and give them all the prizes. What is the paltry emolument of two thirds of prizes to the finances of this vast continent? If so poor a resource is essential to its independence, in sober sadness we are involved in a woeful predicament, and our ruin is fast approaching. The situation of America is new in the annals of mankind elyze; her affairs cry haste, and speed must answer them. Trifles, therefore, ought to be wholly disregarded, as being, in the old vulgar proverb, penny wise and pound foolish. If our enemies, with the best establishment and most formidable navy in the universe, have found it expedient to assign all prizes to the captors, how much more is such policy essential to our infant fleet! But I need use no arguments to convince you of the necessity of making the emoluments of our navy equal, if not superior, to theirs. We have had proof that a navy may be officered on almost any terms, but we are not so sure that these officers are equal to their commissions; nor will the Congress ever obtain such certainty until  see proper to appoint a board of admiralty competent to determine impartially the respective merits and abilities of their officers, and to superintend, regulate, and point out all the motions and operations of the navy."

In another letter to Robert Morris he writes:

"There are no officers more immediately wanted in the marine department than commissioners of dockyards, to superintend the building and outfits of all ships of war; with power to appoint deputies, to provide, and have in constant readiness, sufficient quantities of provisions, stores, and slops, so that the small number of ships we have may be constantly employed, and not continue idle, as they do at present. Besides all the advantages that would arise from such appointments, the saving which would accrue to the continent is worth attending to. Had such men been appointed at the first, the new ships might have been at sea long ago. The difficulty now lies in finding men who are deserving, and who are fitly qualified for an office of such importance."