Bacon's Shakespeare plays as part of The Great Instauration

Sir Francis Bacon

Francis Bacon was the first-born, unacknowledged son of Queen Elizabeth Tudor and Robert Dudley, the Earl of Leicester. He was born on Jan. 22nd, 1560-1. Bacon's parents were wed on two separate occasions: once while Queen Mary was on the throne and the two were imprisoned at the Tower, and a second time after Queen Elizabeth's accession to the throne at the house of Lord Pickering in Sept. and three weeks after Dudley's wife, Amy Robsart's, mysterious death. Lady Anne Bacon, wife of Sir Nicholas Bacon, the Lord Keeper of England, was the Lady-in-Waiting at the time. The Bacons were given the child at birth to be reared in their home, York House, which was next door to the Queen's palace, York Place. When Francis was about 16 years of age and studying law at Grey's Inn,  he discovered by chance about his royal birth. Queen Elizabeth almost immediately sent him off to the Court of France with Sir Amyas Paulet. After spending three years in the splendid but corrupt court of Henry III, he travelled extensively through Germany, Spain, Italy and other European countries studying their manners, customs, politics, policies and religions. During his travels he learned the art of secret writing, purposeful misprints, watermarks, hieroglyphics, headpieces, tailpieces and symbolic pictures. He was also initiated into the Knights Templars.
At a very young age, twelve or thirteen, while he was attending Cambrige University, he had conceived a plan for "The Reformation of the Whole Wide World." This plan transformed into what he afterward called The Great Instauration. "Bacon's brainchild is his Great Instauration, a project he conceived for the step-by-step restoration of a state of paradise upon earth, but coupled with the illumination of mankind. In other words, whereas mankind was innocently ignorant in the original paradise, in the future paradise all human souls will have reached a state of knowledge of truth. Such illumined knowledge will be one based on experience or practice of the truth, which truth (as all great Masters teach, including Bacon) is love—for it is one thing to speak of love and believe in it, but quite another to really know the truth of it." (www.fbrt.org.uk). 
The Instauration includes six parts: 
1. The Divisions of the Sciences 
2. The New Organon; or Directions concerning the Interpretation of Nature
3. The Phenomena of the Universe; or a Natural Experimental History for the Foundation of Philosophy
4. The Ladder of the Intellect
5. The Forerunners; or Anticipations of the New Philosophy
6. The New Philosophy; or Active Science
You can find this list and Bacon's in-depth description of each part in his "Arguments of the Several Parts."

Headpiece from Francis Bacon's original
edition of The Great Instauration

Bacon struggled in his efforts to convey his knowledge to mankind and he began to have doubts that "it flew too high over their heads." At the time, bear baiting and playhouses were popular. He discovered that he could convey knowledge and information to the general public embedded in plays. On these plays he could not attach his name. To be a playwright in those days was not a reputable occupation. Bacon strove for and obtained a high position at court. If his name was attached to the plays he would be met with opposition and personal discredit. In addition, it would destroy his entire plan for the Great Instauration. A pseudonym was the perfect plan to protect all of these elements. 
William Shakespeaere was an actor from Stratford-upon-Avon. Bacon paid Shakespeare for the use of his name on Bacon's plays. As Shakespeare became weathier, he purchased the largest house in Stratford and a coat of arms for himself. 
Bacon also ensured that his knowledge would endure time for the benefit of future generations. He embedded cyphers into his works for future generations to discover and learn about. He created a secret society in which he entrusted his secrets and knowledge. He created a time capsule that he buried in a vault to be opened in a distant future age.

"I have held up a light in the obscurity of Philosophy, which will be seen centuries after I am dead. It will be seen amidst the erection of Tombs, Theatres, Foundations, Temples, of Orders and Fraternities for nobility and obedience—the establishment of good laws as an example to the World. For I am not raising a Capitol or Pyramid to the Pride of men, but laying a foundation in the human understanding for a holy Temple after the model of the World. For my memory I leave it to Men's charitable speeches, to foreign Nations and the next Ages, and to my own Country after some Time has elapsed." --Francis Bacon, Advancement of Learning, Bk II.