class User
  include Mongoid::Document
  
  embeds_many :pets
  
end

class Pet
  include Mongoid::Document
  include Mongoid::Paranoia

  embedded_in :user

  field :species
  
end

ruby-1.9.3-p125 :019 > User.count
 => 1

ruby-1.9.3-p125 :020 > User.first.pets
 => [
   #<Pet _id: 4fabed13d5c23c168b000001, _type: nil, deleted_at: 2012-05-10 16:30:41 UTC, species: "dog">, 
   #<Pet _id: 4fabed24d5c23c168b000002, _type: nil, deleted_at: nil, species: "dog">
   ] 

ruby-1.9.3-p125 :021 > User.where('pets.species' => 'dog').count
 => 1

ruby-1.9.3-p125 :022 > User.where('pets.species' => 'dog', 'pets.deleted_at' => nil).count
 => 0