Board Thread:Questions and Answers/@comment-25066086-20140820174404/@comment-25470191-20141002003657

Lelouch made a request to "C's World" - the result of which was absorbing his mother and father, or possibly removing them from existence as their desires conflicted with the request. Under this, you can assume they were absorbed or dispersed or removed from existence entirely, but this was not Lelouch's request, it was a consequence, the same way as if he used his Geass to tell someone to drive at top speed into a wall, death is likely to occur but that is not the actual request and the victim could survive it.

This interpretation would mean Lelouch is not responsible, the collective unconscious was as it may or may not have been necessary to remove Marianne and Charles.

Charles however may have been killed by Lelouch as the final words spoken to him were "Be Gone". This is while Lelouch had "full power" Geass in both eyes. This was an order which may have been the cause of his death as Lelouch at this stage was powerful enough to kill one with Code.

This turns into a slightly more complicated answer from here:

In theory, Code users are immune to the Geass they grant others. This could be that they are immune to all forms of Geass or they are immune when the holder of the Geass has not obtained a high enough power to kill one with Code.

If they are immune to Geass, Lelouch should not have been able to order Charles to kill himself (after he obtained V.V's Code). Charles may have acted this out anyway or Lelouch may have missed and he acted it. If he acted it out and it was not strong enough at that moment, he may still be able to use it again on him later when it definitely was strong enough.

As there is no previous instance of Geass being used on a Code holder that I am aware of, there are numerous possibilities including death resetting the 1 use Geass option even if resurrection follows, which would leave Charles' death to be directly caused by Lelouch.

As with many things, it's a matter of interpretation. To summarise, the options are:

Lelouch's request to God/C's World/ The Collective Unconscious caused the deaths and he is directly responsible

As above but he is indirectly responsible (unintentional outcome of his request)

Directly responsible for Charles due to "Be Gone" order (indirectly for Marianne)

Indirectly responsible for Charles, "Be Gone" order failed due to immunity or previous use of Geass on Charles.

I think that covers the way I interpreted the possibilities. Be aware that, regardless of the responsibility, Lelouch could still have absorbed/taken/been given Charles' code through the final contact and also that while they vanished, this may have been the will of the world, could have been the interpretation of Lelouch's request by the world or could've just been the way magic stuff works in the Geass universe.

Sorry for the long response and that it doesn't actually provide an answer, only some viewpoints. I like to believe Lelouch took Charles' Code and made the request knowing the only possible outcome (thus holding direct responsibility as it was intentional).