Why is Shakespeare so strongly linked with certain manuscripts of Francis Bacon?

The handwriting expert, Charles Hamilton, was a specialist in old documents and their authentication.  He uncovered a number of forgeries - most famously those of the so-called Hitler Diaries, whose content had (in innocent error) been authenticated by a prominent historian. During the course of these pursuits over many years, he examined thousands of Elizabethan and Jacobean manuscripts.  He came to the conclusion that the same hand had penned each of the following passages:

1)  The whole of Shakespeare's Last Will and Testament, dated 25 March 1616 (which was also signed "by me", a customary declaration of the time, according to Hamilton, that foregoing script was autography).
2)  The 3 pages (plus 3 lines on a fourth) contributed by "Writer D" to the British Museum's 16th century manuscript of a play,
The Booke of Sir Thomas Moore.
3)  Drafts of three applications for Grant of Arms for John Shakespeare (two dated 1596 and one dated 1599 - preserved at the College of Arms).
4)  Some of the wording on the cover sheet of the undated
Northumberland Manuscript, plus one and a half pages within the voluminous contents of that manuscript, which consisted of copies of certain works by Francis Bacon.
5)  The Welcome Enclosure Agreement between William Shakespeare and William Replingham (an attorney acting for Arthur Mainwaring, steward of the Lord Chancellor, who was lord of the royal manor of Stratford).  This agreement, dated 28th October 1614, protected Shakespeare and his cousin, Thomas Greene, both landowners and tithe holders, in relation to the proposal to enclose the common fields at Welcome.
6)  The manuscript of an anonymous, untitled play held in the British Library, commonly known as
The Second Maiden's Tragedy.

The wealth of handwriting evidence offered by Hamilton in support of his expert opinion has been given little, if any, weight by most Shakespearean commentators, probably because the experience required to authenticate it is so scarce.  Also, his focus on Shakespeare's last will and the circumstances of the poet's death allowed critical attention to be directed into side-issues - an unfortunate distraction, considering the significance of the central thesis above.

The work of Elliott and Valenza has shown that Item 6 above,
The Second Maiden's Tragedy, is highly unlikely to have been authored by Shakespeare (based on a statical assessment of authorship traits manifested in that work and in the First Folio). Consequently, if Hamilton is right as to the penmanship, there would need to be explained why Shakespeare should have copied out the play of another author. One or two other elements of the above construction have also been challenged, either on partially conflicting evidence of another nature or on a small number of isolated handwriting features, perceived as anomalies (though Hamilton demonstrated very clearly that individual characters and isolated script, such as signatures, often show remarkable variation in the hand of the same author).  However, there has been no rigorous examination of all his evidence and of his principal discovery (as I have summarised it above) by an appropriately qualified handwriting expert.  Given its value, even if only parts of the discovery were independently validated, this absence is a pity.  But absence also means that Hamilton's specialist evidence and expert opinions (mainly presented and supported in his book In Search of Shakespeare) cannot reasonably be dismissed as worthless.

The Northumberland Manuscript cover sheet (see item 4 of the above summary) appears to have been used as an informal protective cover for accompanying works of Francis Bacon (these being copied in more than one hand - none of which are Bacon's).  The sheet is covered in doodles and scrawls in more than one hand.  It records a mixture of names and/or associated works of authors, including Francis Bacon and William Shakespeare (each written many times), plus Thomas Nashe and Nevill (sic).  Baconians cite it as evidence for their theory that Bacon wrote Shakespeare.  It is similarly invoked by champions for the authorship of Sir Henry Neville and William Stanley, Earl of Derby.

Francis Bacon is known to have employed scribes during the 1590s.  His compositions in their circulated form were written in a hand (or hands) clearly different to that of his personal correspondence.  And, within a lengthy letter to his brother, Anthony, dated 25th January 1595 (modern dating), he wrote, asking for more work for his scribes: 
"I have here an idle pen or two specially one that was cozened, thinking to have got some money this term.  I pray you send me somewhat else for them to write out beside your Irish collection which is almost done."

The handwriting attributed by Hamilton to Shakespeare differs from that of Bacon.  On the basis of its presence in the Northumberland Manuscript, Hamilton theorised that at some point Shakespeare was employed by Bacon as a scribe, contributor and copyreader.  It was this association,  he suggested, which led to the doodled profusion of cover sheet references to or by Shakespeare.  In these doodles the spelling of Shakespeare's name accords with the version now most familiar to us - the one he adopted for his first published work, Venus & Adonis.  Indeed some of the doodled repetitions of the name look like practices of this rendition; all of which suggests that they were scribbled during 1593 or, perhaps, 1594.  Another suggestion of this period is the presence within the doodlings of a variant of a line from Lucrece (entered in the Stationer's Register in May 1594 and published during that year).

Hamilton's interpretation also fits smoothly with the history discovered in the Biography in Shakespeare's Sonnets
. Shakespeare had an intimate, up-and-down relationship with Henry Wriothesley, third Earl of Southampton, to whom he dedicated Venus & Adonis and Lucrece. Whether from solicitude or contrition from his failures to support, the then cash-strapped Earl would probably have been moved to seek for his poet-admirer an alternative source of income at a time of severe hardship in the theatres.

As it happened, the Earl was well connected to place Shakespeare with Francis Bacon.  One route might have been via his guardian, Lord Burghley, who was also Bacon's uncle by marriage.  However, as is brought out in Shakespeare: a Hidden Life Sung in a Hidden Song, the young lord's relationship with Burghley was by then strained.  A more likely route would have been via Southampton's great friend and role model, the Earl of Essex, who was then Bacon's champion, employer and financial supporter.

Bacon's pen "that was cozened" might even be a reference to an embittered Shakespeare, who had not been rewarded properly for his dedications of
Venus and Lucrece.  This construction is perhaps weakened by the re-opening of the London playhouses some months prior to the date of the letter.  But it does accord with the situation discernible in the Sonnets and with the suggestions in Bacon's wording that there was something unusual about the employment of this scribe and that this background was known to his brother.  Bacon's message can be interpreted as:  "In particular, I continue to have surplus copying capacity because Shakespeare hasn't received the money he was promised and therefore I am still saddled with him".

There remains in existence a note-book of Bacon, which he called his
Promus of Formularies and Elegancies.  It contains writing in at least one hand other than Bacon's - suggesting that it was accessible by persons other than the philosopher.  From internal evidence, it was commenced no later than 1594 and perhaps earlier.  It records many proverbs, adages and other verbal expressions, often derived from other authors.  A significant number of these expressions - or close parallels - are to be found in Shakespeare's later works (but often not in Bacon's).  Baconians regard such coincidence as further powerful evidence in support of their theory, since, they argue, Shakespeare could not have seen the Promus.

However, with Shakespeare in Bacon's employment, as suggested by Hamilton, he would have been in an ideal position to have had access to the
Promus, particularly if, at times, his pen was "idle".  He may even have been responsible for some of its contents, by way of directed research or otherwise.  In any such event, he would likely retain memorable words or phrases for subsequent use - and perhaps even record them in his own version of the Promus.  Shakespeare had a propensity to mine the works of others, as shown by the close parallels in many of his plays with earlier pieces.  And his territory was not confined to long dead authors.  Marlovians discern as many parallels in his works with those of his close rival, Christopher Marlowe, as do Baconians with those of their favourite.

The separate strands of evidence, described above, combine to support the premise that William Shakespeare worked for Francis Bacon during a period (or for periods) within 1593-5, and that he thereby gained access to certain of Bacon's works.  Though the evidence is circumstantial, it is contradicted by nothing in the histories of either man.  At worst it nullifies any argument that only Bacon's authorship of Shakespeare can explain the connections with the
Northampton Manuscript, Promus or any other works of the philosopher.  More likely and excitingly, it invites further discovery of the real Shakespeare: the man with unique connections, who is revealed in Shakespeare: a Hidden Life Sung in a Hidden Song.