The ending is something of an homage to The Godfather; as Elizabeth I remakes herself into a secular deity to lead England, she's commanded "let it all be done", causing her master of spies, Walsingham, to orchestrate a stunning series of assassinations, brutally executing her enemies and consolidating her power.
Depending on your background, you may consider it a Downer Ending.
Elizabeth getting The Act of Uniformity passed through Parliament. Walsingham helped by temporarily locking some prominent churchmen in the basement until the voting was finished.
Walsingham torturing the priest sent to kill his Queen.
At the beginning of the movie, Elizabeth is a prisoner of her half-sister Mary, who is being encouraged by her advisors to have Elizabeth executed. Elizabeth, though terrified, manages to hold on to her courage when sent to Mary to beg for her life.
Mary: When I look at you, I see nothing of the king; only that whore, your mother. My father never did so well as to cut off her head.
Elizabeth: Your majesty forgets, he was also my father.
The Golden Age
"I too can command the wind, sir! And I have a hurricane in me that will strip Spain bare if you dare to try me!"
Clive Owen's monologue on crossing the North Atlantic (taking words from Sir Francis Drake). The music and the "ascending to heaven" metaphor make it very beautiful indeed.
Sir Walter Raleigh: Can you imagine what it is to cross an ocean? For weeks, you see nothing but the horizon - perfect and empty. You live in the grip of fear: fear of storms; fear of sickness on board; fear of the immensity. So you must drive that fear down, deep into your belly; study your charts; watch your compass; pray for a fair wind; and hope. Pure, naked, fragile: hope. ... At first it's no more than a haze on the horizon. So you watch. You watch. Then it's a smudge; a shadow on the far water, for a day ... for another day. The stain slowly spreads along the horizon, taking form ... until, on the third day, you let yourself believe. You dare to whisper the word: land. Land. Life. Resurrection. Coming out of the vast unknown, out of the immensity ... into new life. That, your Majesty, is the New World.
The Queen staring down the barrel of a gun and refusing to back down.