I believe that the mother died in childbirth and that is why she never returned. All of the folklore is a parallel of Ben's life. Macha the witch is Ben's grandmother, Seanachai is the ferryman, Machaleer (the Giant) is Ben's father. Macha tried to ease her son's inconsolable grief in much the same way that Ben's grandmother tries to help her son end his grief by showing him that living in the lighthouse is surrounding himself in the past and its sadness. Ben turns to fantasy as a way to cope with his mother's death, forgive his sister for what he sees as taking his mother away from him, and awake his father from his grief of living in the past. I think this sort of dual-story was intended by the writers, if you look up the Yeats poem that is quoted at the beginning of the film, you will see that it is about a child turning to fantasy because the heartache and trouble of the world is too much for him to bear or to understand:


> ### *Stolen Child*, by W.B. Yeats 
    
> Where dips the rocky highland  
> Of Sleuth wood in the lake  
> There lies a leafy island  
> Where flapping herons wake  
> The drowsy water rats  
> There we've hid our fairy vats  
> Full of berries  
> And of Reddest Stolen Cherries.  
>  
> Come away oh human child  
> To the waters and the wild  
> With a fairy hand in hand  
> For the world's more full of weeping  
> Than you can understand  
>  
> Where the wave of moonlight glosses  
> The dim grey sands with light  
> By far off the furthest roses  
> We foot it all the night  
> Weaving olden dances  
> Mingling hands and mingling glances  
> Till the moon has taken flight  
> To and fro we leap  
> And chase the frothy bubbles  
> Whilst the world is full of troubles  
> And is anxious in it's sleep  
>  
> Come away oh human child  
> To the waters and the wild  
> For the world's more full of weeping  
> Than you can understand  
>  
> Where the wandering water gushes  
> From the hills above glen car  
> In pools among the rushes  
> That scarce could bathe a star  
> We seek for slumbering trout  
> And whispering in their ears  
> Give them unquiet dreams  
> Leaning softly out  
> From ferns that drop their tears  
> Over the young streams  
> 
> Come away oh human child  
> To the waters and the wild  
> For the World's more full of weeping  
> Than you can understand  
>  
> Away with us he's going  
> The solemned eyed  
> He'll bear no more the lowing  
> Of the calves on the warm hillside  
> Or the kettle on the hob  
> Sing peace into his breast  
> Or see the brown mice bob  
> Round and round the oatmeal chest  
>  
> Come away oh human child  
> To the waters and the wild  
> For the world's more full of weeping  
> Than you can understand  
> 
> For he comes, the human child  
> To the waters and the wild  
> With a faery hand in hand  
> For the world is more full of weeping  
> Than you can understand