You've killed us both

[thePyro13]

I don't think The Shadow is a guardian. After all, Weyer managed to remove several orbs from their resting places without invoking the shadow.

It is. Weyer was just pretty strong person (spiritually/mentally) and thus was able to hold many Orbs.

I don't remember reading or hearing anything like that in the game. Where did it say this? And this could also be attributed to Weyers knowledge and skill with the orbs, Agrippa did state that Weyer had surpassed him as his student.

I think it is a side effect of someone who is not skilled with the orb trying to use its power. It chased Agrippa when he first activated one, and daniel, but not Alexander, or Weyer.

It chased Agrippa? H, don't remember this one.
Regarding "using Orb's power". When Daniel first time saw it, he has NO idea what is this and how to "use " it. But Alexander knew and he has a plan & knowledge how to use it's power. But in the end, it's Daniel who were being chased by Guardian, not Alexander. Why?
The answer is simple: Orb exist to be used. But only by a person who has enough power to do so. Even an innocent child who touched the Orb can be killed by Shadow just because he is small and weak. It is not a matter of justice or sumtin, it's a "nature/balance force" as Alexander says.

Agrippa talks about it in the letters he sends to alex(you can find them in the study, I think).

Daniel 'used' the orb just by touching it. The shadow chases him because he isn't powerful enough/doesn't know how to use it.

Like I said, I think the shadow didn't chase Alexander because he knew how to use the orb properly.

Ending 2: Daniel lets Agrippa through the portal. He still hasn't faced what he has done, the shadow consumes him, and Alexander. Though in the end we hear Agrippa plead to Weyer to save Daniel, so we don't know for sure of daniels fate.

If Shadows kills Daniel HOW Ahrippa 7 Weyer saves him?
No answer.

Aprigga and Weyer are on the other side of the portal. Who knows what's over there, it could be an immaterial realm. Weyer is capable of travelling through the cosmos with the orbs he possesses(as claimed by Agrippa), who knows what he is capable of. That and the fact that you(the player) are overhearing this conversation might suggest that Daniel is not quite dead yet. And may still be saved. In such a way similar to the fact the Agrippa was just a head, and yet has clearly survived.

Ending 3: Daniel places the blame for everything he has done on Alexander, and ruins Alexander's plans. He wants Alexander to pay for what he has made Daniel do. He breaks the portal, and the shadow consumes Alexander. Daniel feels as though he has received justice for what happened at the castle and the shadow retreats.

Alexander used first Orb's power (Agrippa's one) and NO Shadow was haunted him . Why? It supposed to. Now, he uses second Orb and NOW Shadows kills him.
Really? REALLY?
It makes no sense at all.

The shadow killed him because Daniel felt that he was the source of all his guilt. The shadow was still the one that Daniel had 'created' when he first used the orb.

Alexanders death has nothing to do with him using the orb, but with Daniel confronting him. After all, Alexander sent Daniel away so that he wouldn't lead the shadow to him.