Death Busters
The primary antagonists of the Infinity/Super arc are what is collectively known as the Death Busters. Originally from another dimension, the Death Busters came to Earth to assimilate the planet into their "Tau System," receiving help from Soichi Tomoe, Hotaru's father.
At the age of eight, there was an accident at her father's laboratory. Her mother was killed and Hotaru herself was gravely injured. She should have died as well, but her father rebuilt her body with machines, so she is part human and part machine - a cyborg. This is something that plagues Hotaru for the rest of her life - she should have died in the accident, but was forced to live. Her existence as part-machine is painful and tortures her, and no one outside of her family knows about it. She doesn't want them to know, and covers it all up as best she can. As the Outer Senshi later explained, her body was falling apart and the only way to save her would be for her to awaken as Sailor Saturn.
While her father was constructing her body, the Death Busters came to Earth. Hotaru's father, consumed by his research on "Super Beings," eagerly took what they had to offer. He became half alien and half human, taking his precious research further. With newfound powers and resources, Hotaru was made into a Vessel, planting an daimon egg into her.
As Hotaru grew older, the planted alien sapped Hotaru's strength. She frequently experienced "attacks" and sometimes lost consciousness, taking on a more evil appearance and sometimes the alien inside her would actually speak. She had the ability to heal wounds (although it's unclear to me if this was due to the Death Busters or Sailor Saturn). She continued living in this pathetic existence until she discovered Chibiusa's Ginzuishou, which carried a power that roused the alien. Finally, it was able to take control of Hotaru's body.
The alien manifests itself as Mistress 9, appearing as an older version of Hotaru with long hair. Mistress 9 takes Chibiusa's Ginzuishou and with it, Chibiusa's soul. Hotaru should have disappeared when that happened, especially with the massive surge of power Mistress 9 absorbed from the Ginzuishou, but her soul remained though her body was taken over. In this form, she sees her father give into madness, learns the truth behind his actions, and watches the Sailor Senshi defeat him.
In addition to the Ginzuishou, Mistress 9 takes the souls of the four Inner Senshi. Hotaru fights to protect them though, but she wonders why she keeps fighting when she has nothing left, and it is the force of Sailor Saturn that compels her to keep going.
Papa is gone. There's nothing left for me, so why do I still have this power? Was I really this strong? ... I can feel a greater Self deep within me. That Self is telling me ... "You must stake your life to save them." ~ Hotaru, Act 33
Hotaru manages to protect all five souls and returns all of them, leaving her body in the process. However, this means that she is unable to prevent Mistress 9 from escaping as well. When Mistress 9 finally shreds through Hotaru's body to assume her alien form and go to Pharaoh 90, Hotaru disappears - an indication that Sailor Saturn would soon appear.
The circumstances are a little different in the anime. Hostes (souls) from the manga have been changed to "Pure Heart Crystals," which are actually crystals rather than abstract balls of light, and they look like the brooch on Saturn's uniform. In the anime, Hotaru's soul fades in and out of consciousness. Her father does not die - rather, the alien separates from his body and he returns to normal. She finally overcomes Mistress 9 with the affirmation that she has people she cares about: her father and Chibiusa. Once Mistress 9 is gone, Sailor Saturn awakens and returns Chibiusa's Pure Heart Crystal.