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 Alyssa must uncover her family's secrets.
Alyssa Hamilton is the protagonist of Clock Tower 3.   She is  British girl nearing the age of fifteen and is attending boarding school at the game's outset.  Alyssa, her mother, and all of the females in their ancestry possess special abilities to do battle with shadowy beings known as "Entities" and their underlings the "Subordinates".  Alyssa has a respectful and mature demeanor as well as a since of family duty and honor.

Story (spoilers below)

 Alyssa has great respect for the dead and goes to great lengths to bring their spirits' peace.
Alyssa's father, Philip, died while she was very young.  This led her to be raised by her mother, Nancy.  In this single parent home, Alyssa matured quickly took on more responsibility than the average child.  She was not without a father figure, however, as she was very close to her grandfather, Dick (Nancy's father).  Her grandfather was even the one that chose Alyssa's birth name.
 
 As a Rooder she has a magical bow to fight off the killers.
Throughout the mystery in Clock Tower 3, Alyssa learns many things about her family and ancestry.  The women of her bloodline are part of a special group of humans known as "Rooders".  These women contain special abilities that allow them to do battle with evil beings known as "Entities" which are generally possessed and resurrected serial killers.  A Rooder's abilities peak at the age of fifteen and they eventually dwindle to nothingness at about the age of twenty.  At this point in a Rooder's life, they are expected to sire another daughter in order for the line of Rooders to continue.  Nancy Hamilton sent Alyssa to boarding school in order to shield her from the life of a Rooder and that she might age peacefully past the age of fifteen and never have to do battle with any Entities or their Subordinates.
 
 Alyssa must evade her foes until she puts the victims to rest.
One of the darkest mysteries that Alyssa uncovers is the fate of her father.  Dick, her grandfather, was obsessed with protecting the Rooder bloodline and carefully oversaw his daughter Nancy's courtship and wedding.  He was unhappy with her choice in Philip but acquiesced and accepted the marriage simply to allow the bloodline to continue. However, he quickly became frustrated with the man's lack of dignity or honor and shamed the Hamilton name.  Dick felt that Nancy was even being influenced by Philip, saying that she did not want Alyssa to be raised as a Rooder.  In order to protect the sanctity of the Rooder line, Dick pushed Philip over the balcony at the family estate.  Philip fell over and landed near the wood-chopping stump.  His head was sliced open by an idle axe's blade.  Alyssa witnessed these events as she traveled in time while doing battle with the Axeman.

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