Drake visits the ailing colonists with a view to rescuing them, but he has not counted on their determination in the face of attacks by the indigenous tribes.
Spymaster Francis Walsingham forges letters plotting against Queen Elizabeth to incriminate the imprisoned Mary Queen of Scots. Suspicious of his motives, Elizabeth sends Drake undercover to investigate.
An astrologer by the name of Doctor Dee is adviser to Queen Elizabeth, but his advice on the stars is not good news for Drake, who wants to sail to Ostend to rescue English prisoners. The Spanish Ambassador to England had a hand in this fake bad news and Drake wants to set the record straight in order to complete his mission.
The queen sends Drake to Calais to rescue Lord Oakeshott, an English gentleman being held there on a charge of murder, but when Drake gets there he finds that Oakeshott is not a prisoner and appears to be a free man under the protection of a Countess. A lovesick young fool, Oakeshott is unwilling to leave.
Queen Elizabeth sends her godson Master Harrington on a mission as an emissary to deliver a message to her Portuguese ambassador, but learns en route that Philip of Spain has invaded Portugal. She must get word to Drake before Harrington lands and is captured. The English Ambassador to Portugal is being held prisoner by the Spanish and Drake must get him and Harrington back to England.
Drake takes provisions to Belgian garrison of Blankenberge where there are supposed to be 500 English soldiers ordered to keep the Spanish at bay. On arrival he finds that most of the men have died and their are only around 13 men left. While the men are dying of starvation their Spanish enemies are well fed and supplied, so Drake decides to destroy a bridged causeway that is being used to supply the Spanish. The remaining men are returned to England where the garrison commander Captain Williams is honoured by the queen.
An inventor demonstrates a flame-thrower, which he plans for peaceful purposes: clearing land of weeds so crops can be grown. But the Queen demands he turn it over to the military. The Spanish try to trick him into giving them the secret.
Stukely, possibly an illegitimate son of Henry VIII, is given permission by the Queen to found a new country in the New World, with him as King. Encountering problems with both his settlers and the Spanish, Drake comes to his assistance.
The Queen promises a Spanish treasure ship safe passage through the English Channel, leaving Drake with the dilemma of how to capture the gold without breaking Elizabeth's word.
Hugh Graveney, a Drake lookalike, uses a ship similar to the Golden Hind to seize loot from a surrendering Spanish ship then proceeds to slaughter all Spanish hands. What is thought to be the Golden Hind is eventually captured and when the Spanish realise who they have, the Spanish Ambassador uses him to turn the Dutch against England. Drake must convince the Queen that he took no part in the treachery he is accused of and sets out to catch the imposter.
Spain invades England's oldest ally Portugal, and imprisons its most active leaders in Castle Ortega. Artist and soldier Pedro de Vazim escapes and makes his way to England where the Queen enlists the help of Drake to secure the release of the Portuguese resistance leader Gazio. Drake, Gazio and de Vazim's sister Maria devise a plan to cross a castle bridge to make good their escape as the Golden Hind destroys the castle's cannon defences.
Queen Elizabeth is in love with the French Duke Alencon, and hopes to receive a marriage proposal. However since his return to France she has heard nothing further from him and suspects that his mother the French Queen Catherine de Medici has something to do with it. Elizabeth sends Drake to France to investigate. The French queen will stop at nothing to keep Drake from discovering the truth - that she has imprisoned her son in the Bastille to prevent any union with Elizabeth.
The Spanish want to invade England overland but the small area of Ravenstein (in Holland) stands in their way. Elizabeth sends Drake to bring the Duchess back to England so the Spanish cannot use her to threaten her people.
Drake rescues a boatload of gypsies, who, by their own account, were mercilessly abandoned in the sea by a ruthless Spanish ship's captain. However when Drake discovers the Spanish captain adrift in a boat he finds that the gypsies are not as innocent as they claim and must act before he and his crew suffer the same fate as the Spanish ship and her crew.
