There has been a lot of confusion about the ending and i personally was very confused when the game finished but when i think about it there are only a few possibilities.I have copied some of the stuff from the walkthrough on neoseeker.com which beautifully explains the game.
Why is the game called Penumbra?
A 'penumbra' is the name given to one of the three parts of a shadow,particularly those cast from celestial objects, like the sun or moon.A penumbra is the partially concealed part of the shadow, where a section
of the light source is obscured.
Given the mysterious nature of Black Plague, the penumbra would seem symbolic for the hidden truths that Philip is searching for. It represents the uncertainty in Philip's mind, and indicates the dark atmosphere of the
game - both visually and thematically.
What do we know about Philip?
Not too much is revealed about our protagonist, even over two whole games.From the first episode, Overture, it seems that Philip is English, probably living in, or close to, London (Mayfair, where Philip retrives his father's deposit box, is in the Westminster area of London). Philip is voiced by an English actor in Overture, although this changes to a North American voice actor for Black Plague. Presumably this was down to contractual reasons,rather than some kind of elaborate disguise by the character.
Philip's surname is given as Buchanon in Overture, yet according to Black Plague, his father's name is Howard LeFresque. We also know that Howard left Philip before he was born - this would suggest that either Philip's parents were never married, or they had divorced before his birth. Either way,Philip wasn't brought up in ideal family circumstances.
Perhaps this also explains why Philip seems to tell no one about his trip certainly the tone of the email he sends at the end of Black Plague suggests that the recipient is the first and only person that Philip confides in.
This would also indicate he has no family to speak of, and no incentive to stay in his former life. Loneliness seems to be a recurring theme in the series - not once does Philip come face-to-face with another recognizable
person, for example. The corridors in Overture also serve to dwarf Philip in size, perhaps underlining the perceived insignificance of his existence.
What did the ending mean?
The final words of the game are relayed by Philip in an email to an unknown recipient. In it, he speaks of the request made by the Tuurngait to him - to destroy the facility and bury the alien virus. Philip, however, reveals
the location of the mine in the email and asks this unknown person to "kill them all". Why he would do this raises some interesting questions.
Philip (and the Tuurngait previously) speaks of humanity being dangerous as a group, yet intelligent as individuals. The Archaic, as a group, sought to control and use the Tuurngait - whereas Howard and Philip, as individuals,are chosen to protect it.
Howard asked his son to burn all the evidence in the first game.He did this so that the last link to anyone finding this dangerous place is erased and so that this secret is left buried in the snow.This way the Tuurngait would not be disturbed and wouldn't be angry and live in peace and no human would be harmed too.But As Philip says in the email "Human nature sealed my downfall".This means that his curiosity got the better of him and he started investigating eventually reaching Greenland.The reason he did this was not because he was just curious but because this was the last thread that linked him to his father.He had never heard from him and now he sends him a mysterious letter from beyond the grave,obviously he was going to investigate.
Tuurngati is an ancient entity that came to Earth millions of years ago; it once co-existed peacefully alongside the native Inuit, using "Infected" host bodies to pass its ancient knowledge to mankind. However, in time mankind began to grow and expand, and the Tuurngait burrowed underground to separate itself from the human world. When the Archaic came, they disturbed the Tuurngait's ancient slumber and attempted to exploit it, and it fought back against them in self-defense. The Tuurngait explains that mankind is intelligent and compassionate as individuals, but selfish, petty, and destructive as a whole. However, it believes that Philip is different from most of mankind. The Tuurngait puts itself at Philip's mercy, asking him to send a message to someone above ground, for them to destroy all information regarding the Archaic's research facility so that the Tuurngait may rest in peace. This is the same request the Tuurngait made of Philip's father Howard, however Philip thwarted it by coming to investigate instead of following his father's instructions.
So Howard did what was required of him and then he died.But as Philip said,hewould not make the same mistake his father did.This means that he would not follow the Tuurngait's order and that he would do the opposite.The main suspense is WHY?.Why did Philip choose to do this?There are two theories for this :
The most likely theory according to me is that Phillip had witnessed a lot because of the Tuurngait and the virus.He had watched his loved ones die.His father Howard died because of it.He was forced to burn his only friend,Red who helped him survive and he was lead into killing Amabel too.This had greatly affected him and Clarence was just a summation of all his negative thoughts.This does not mean that Phillip was never possessed,he was but Clarence was just bringing out his most negative feelings.Philip may also be angry about how he was made to pass tests by the Tuurngait like a lab rat.The turngait are like the reverse of humanity.Humanity is peaceful and intelligent as individuals but dangerous as a whole but the Tuurngait is dangerous as individual but peaceful as a whole.Maybe Philip does not agree with the Tuurngait's views.And maybe he wants revenge.The experience over the games transformed him.He himself said that he is much more like Clarence.So he wants revenge by killing the Tuurngait.
Another theory might be that the motive for sending the message out would be to purposely expose more humans to the virus. Howard displays great remorse and shock in his Final Words note, when he learns that the Tuurngait was simply defending itself, and it seems reasonable to suggest Philip would have a similar reaction when he is told the truth. Perhaps the anger towards the Archaic group, and humanity in general, would cause Philip to justify a desire to bring humanity and the Tuurngait crashing together. The 'kill them all' could be, in fact, a misleading instruction - it's humanity he wants destroyed,not the Tuurngait.I don't think this is very likely.Phillip lost had formed many bonds with various humans like Red and Amabel over the game and so i don't think he would start hating humanity rather than hating the Tuurngait who were responsible for these deaths.
If you have some other theories or ideas please feel free to share them