Lost Kingdoms takes place in the world of Argwyll, where a mysterious black fog has started sweeping over the land. Nothing consumed by the fog has returned, and it threatens to destroy the entire world.
In the nation of Alanjeh, the king has left to meet with the leaders of the other nations to try to find a way to stop the fog. But when the fog reaches the gates of Alanjeh castle, the king has yet to return. Princess Katia, the king's daughter, remembers her father's prior instructions to guard the runestone of Alanjeh with her life, and leaves the castle with the runestone in her possession. The runestone grants her the ability to summon monsters from cards, allowing her to fight the creatures that roam the black fog. Before leaving she meets an old woman named Gurd, who frequently gives Katia information on her next destination, and sells Katia cards from her Apothecary.
Katia journeys to the kingdom of Grayl to look for her father. Upon reaching the castle, she finds that it is under siege by monsters, and they are being led by a woman named Helena, who also has a runestone. She had attacked in an attempt to take Grayl's runestone, but Katia manages to defeat Helena. Helena escapes, claiming that she will see her again. Afterwards, the king of Grayl explains to Katia that her father already left before the attack. He also gives her their runestone, saying it will help her stop the fog and that she must collect the other runestones too.
On her way to castle Whyt, Katia catches up with her father, who is fighting a powerful monster. During the battle he is seriously wounded. Katia manages to defeat the monster afterwards, but she is too late to save her father, and he dies in the field.
After reaching castle Whyt, Katia encounters Helena. They battle again, and Katia defeats her once again. While she is dying, Helena explains that she was the princess of a kingdom far away from Argwyll. One day, their kingdom was overtaken by a man called The Enchanter, who was controlling the black fog. The Enchanter forced Helena to attack Argwyll and retrieve the runestones against her will. Helena asks Katia to stop him, and then she passes away.
Katia travels to Broch Black, the lair of Thalnos, The Enchanter. Katia defeats him, but it is then revealed that Thalnos is merely a vessel for the true source of the fog, the God of Destruction. The God of Destruction attempts to kill Katia, but she defeats him in battle. Afterwards, the fog is removed from Argwyll and the monsters disappear. Katia becomes the queen of Alanjeh and works to restore her kingdom.
Combat revolves around using cards that the protagonist, Princess Katia, uses to summon different monsters. Using these cards requires magic stones. You get more stones by dealing damage to enemies and destroying obstacles. If you run out of stones, you can still use a card at the cost of HP. The more stones you needed to use the card, the more HP drained.
The world map shows the different locations that you click on to enter. More locations become available after you've cleared one, but once you've finished a location you can't enter it again, besides Gurd's Apothecary and Alexander's house. Many of these stages are required to complete to finish the main quest, but many of these locations are optional and contain useful cards.
The monsters that you summon are divided into several types. The weapon-type monster appears and vanishes quickly in front of you launching a single attack, these cards can be used two, three or four times before they can't be used again in that location. The summons-types either deals great damage or heal you, those that damage can only be used once per card in each location. Independent-type monsters act freely and attack your enemies until they either run out of energy or are killed. The spin-type constantly spins around Katia and causes damage to anything near her. Trap-type monsters hide themselves and attack when an enemy comes near enough.
All cards are grouped into one of five elements. These elements are Fire, wood, earth, water, and neutral. Fire beats wood, wood beats earth, earth beats water, and water beats fire. Neutral cards have no positive or negative effects relative to the other elements.
While exploring the environment. There are two kinds of fairies, red and blue. The blue ones have instant effects that either heals you, gives you some magic stones or restores a card. The red fairies you collect and give away to the young scholar Alexander, who gives you very powerful cards in exchange. There are 100 red fairies in the whole game, and Alexander gives you a new card about every 10 fairies. Whenever you find a red fairy it gives you some helpful advice.