To understand Special Counsel Robert Mueller's motives in his investigation, consider another story in which a tyrannical government grilled an innocent to make her confess whatever they wanted to hear.  This is the story of Joan of Arc.

The Hundred Years War was going badly for France. In 1420, French King Charles VI signed the Treaty of Troyes, which made King Henry V of England his successor. In 1422, Charles VI died. This led to a conflict. Is the King of France Henry V (analogous to Hillary Clinton) or Charles VII (analogous to Donald Trump)? The war continued.

Under the cloud of royal uncertainty and possible French defeat, a coronation for Charles VII would have been laughable.  Then Joan of Arc came on the scene.  She correctly predicted the French defeat at the Battle of Rouvray.  She then asked to see Charles.  She convinced Charles to let her lead his army.

Joan led the French Army in the Battle of Orleans.  Between Joan's leadership and English bad luck, the French won on 8 May 1429.  This encouraged the French to crown King Charles VII on 17 July 1429.

Buoyed by victory, Joan felt that she could win in any situation.  She fought to retake Paris but failed.  She fought again at nearby Compiegne and was captured.  She then stood trial for being a witch.

It was important to prove that Joan was a witch.  With such a revelation, one could say that Charles' coronation was a sanction by the devil, not God.  The English could then say that Henry VI (Hillary) was the rightful ruler of France.

Initially, Joan denied that she was a witch.  The trial went on for months.  The English threatened to kill Joan unless she renounced her alleged sins.  Joan renounced them.  A few days later, she had a change of heart and said that she did nothing wrong.  The English concluded that Joan was incorrigible and deserved to die.  She was burned at the stake.

With the loss of Joan of Arc, the war continued until 1453 with the French victory at Castillon.

The most important conclusion of this story is that the English tried to coerce a false confession, since there are no witches, that would unseat a king.

Six hundred years later, in a supposedly more advanced century, Robert Mueller was given a task similar to that of the English.  In the letter giving Mueller Special Counsel powers, Mueller was ordered to seek a link between the Russian government and anyone associated with Trump's campaign.  Apparently, such a link must be illegal if the Justice Department looks into it.  This is clearly not meant to jail associates of Trump.  This is to jail Trump.  This is quite similar to trying to depose King Charles VII.

The associates of Trump who are getting the Special Counsel's focus are General Michael Flynn and Paul Manafort.  The main accusation against Flynn is that he allegedly lied to the FBI on 24 January 2017.  This is in spite of the fact that the FBI reported that Flynn was "relaxed and jocular" and that one of the agents, Peter Strzok, concluded that Flynn was truthful.  The next step was to get Flynn to confess to this crime.  The Special Counsel threatened to investigate Flynn's son if he did not confess.  He confessed.

The Special Counsel is now interrogating Flynn and is asking the judge to delay sentencing.  As long as there is no sentence, Flynn is forced to answer questions.  I assume that the topic is dirt on Trump.  The fact that the questioning continues means that years of questioning have not been sufficient to find the dirt.

Paul Manafort was accused of tax fraud that occurred long before Trump started his presidential campaign.  Manafort defiantly decided to go to trial.  He lost.  Faced with a sentence that would exceed his lifespan, Manafort chose to cooperate.  Manafort is being interrogated, just as Flynn is.  On 26 November 2018, Mueller said that Manafort violated his plea agreement by lying.  His alleged lie is not known publicly.  I assume that Manafort's interrogators are not as patient as Flynn's.

As long as Manafort and Flynn provide no dirt on Trump, they will have their sentences delayed.  As soon as one of them remembers (or makes up) some dirt, he will be given a lighter sentence and the investigation will turn to Trump.  If he later recants his remembrance, he will not be burned at the stake, but he will be punished. 

Defendants are being accused of alleged crimes that occurred either before or after Trump's presidential campaign.  These crimes are not in the scope of the investigation and there was no probable cause to investigate these people for them.  Their crime is that, like Joan of Arc, they know the head of state and an accusation of wrongdoing from one of them would be believed.