The two main characters in Pandora's Tower are Aeron and Elena. Aeron is from the Kingdom of Athos, while Elena is from the Kingdom of Elyria. This makes them an unlikely couple, since the two kingdoms have been at war for a long time.
They met three years before the events of the game in 508, during the war. Aeron was wounded in the war, and he was running through a forest in Elyria. He soon stumbled and fell over. Luckily, he happened to have fallen unconscious not too far from Elena's home. She found him some time later, and took him back to her place. He woke up in her home, and heard Elena and her family talking. Her parents were saying it was very dangerous bringing a soldier from Athos into their house, but Elena was desperate to help him. She said she couldn't just leave him there. This is the beginning of their relationship.
The other main character in the game is Mavda, one of the Vestra tribe. She helps the couple a fair bit. She takes them to the Observatory after the incident at the Harvest Festival, which left them with the entire Elyrian army chasing them.