The Golden Hind sinks a Spanish ship and prisoners are bought aboard. Among them Countess Inez (Natasha Parry) who plans to repay Drake's kindnesses by sinking his ship using a long fuse made by Roberto (Warren Mitchell) from her cabin to the ship's gunpowder stored below. Drake evacuates his ship as time for its sinking comes close, staying on board with the Countess.

Drake pleads the case of the Virginia colony to Elizabeth against Daniel Peters (Charles Lloyd-Pack) who only wants any gold found and wants the colony shut down, and Walsingham (Richard Warner). We see Mendoza (who is the Spanish Ambassador to the court) for the first time. They discover a stowaway aboard on the way to Virginia, (Olive McFarland) who they take to her husband to be Tom Brewster (Barry Foster). The colonists leave as they have had enough of Indian attacks and bad supplies.

Elizabeth is worried about Mary, Queen of Scots (who she eventually had executed) (played by Noelle Middleton). Walsingham decides it is time to get Mary out of the way and has his henchman, Thomas Phillips (Harvey Hall) forge a letter from her to make it look like she wants Elizabeth dead. Drake is sent to check on this but is imprisoned by her captor, Sir Amyas Paulet (Alfred Burke) who is in on the plot too.

Doctor Dee (Raymond Huntley) entertains Elizabeth and her court with some magic tricks. Mendoza's man, Don Pedro steals all Dee's papers and he is forced to make a false astrology chart so the superstitious Queen refuses to allow Drake to sail to Ostend where some Spanish ships are holed up and rescue some English prisoners on them as well as liberating the captured cargo. Drake has to get the papers back for Dee before he can sail.