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The night the dark mark was cast upon the astronomy tower in Half-Blood Prince, Professor Snape stunned Professor Flitwick before joining the battle.

“Outside Snape’s office, yes,” whispered Hermione, her eyes sparkling with tears, “with Luna. [. . . .] It was nearly midnight when Professor Flitwick came sprinting down into the dungeons. He was shouting about Death Eaters in the castle, I don’t think he really registered that Luna and I were there at all, he just burst his way into Snape’s office and we heard him saying that Snape had to go back with him and help and then we heard a loud thump and Snape came hurtling out of his room and he saw us and — and — [. . . .] “I was so stupid, Harry!” said Hermione in a high- pitched whisper. “He said Professor Flitwick had collapsed and that we should go and take care of him while — he while he went to help fight the Death Eaters —” [. . . .] “We went into his office to see if we could help Professor Flitwick and found him unconscious on the floor . . . and oh, it’s so obvious now, Snape must have Stupefied Flitwick, but we didn’t realize, Harry, we didn’t realize, we just let Snape go!”

There were no Death Eaters there to witness, so Snape didn't need to attack Flitwick to act his part. He also didn't stun Hermione and Luna, which would have made sense if he was trying to keep as many innocent people away from the fight as possible. So why?

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    He tells Hermione and Luna to stay where they are, far far away from the action at the top of the astronomy tower. That keeps them safe. – Stephane Mathis Jun 23 '15 at 9:33
  • @StephaneMathis That doesn't answer the Question. As mentioned by the OP Snape didn't know about Hermione and Luna standing around the corner. So Snape did not Stupefy Flittwick so he could tell Luna and Hermione to stay with Flittwick simply because he did not know they were there. The reason for the stupefy, which is the essential part of the question, therefore is not to keep Luna and Hermione safe! – Zanser1609 Jun 23 '15 at 9:48
  • Zanser already answered the case of Flitwick. – Stephane Mathis Jun 23 '15 at 9:55
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I just think it's because he knows that it's about time that he has to take care of his unbreakable vow and his promise to Dumbledore. Therefore he knows that he has to go now and kill Dumbledore as planned.

But how should he get to the Astronomy Tower and do his 'job' without Flitwick following him?

And if he follows him, how should he explain to him what he's about to do? Nobody knows about the plan and it was Dumbledore's will that nobody SHOULD know until the very end. By stupefying Flitwick, Snape acts in the only reasonable way.

He doesn't want to have any of the professors following him on his way up to the Astronomy Tower.

Edit:

As discussed in the comments of this answer it may be a bit harsh to say Snape is stupefying Flitwick because he is going to kill Dumbledore. At that moment Snape did not know whether Dumbledore is already back in Hogwarts. And because the Dark Mark has been cast before Dumbledore and Harry returned, which is also the specific reason why Dumbledore and Harry are flying to the Astronomy Tower and not simply to the Front Door, not even the reader knows whether Dumbledore and Harry are back at the time this happens.

But what we can clearly state is that Snape knew that there was something going on in Hogwarts. So he stupefied Flitwick because if both of them meet the Death Eaters there would be a slightly uncomfortable Situation for Snape as he could not attack the Death Eaters neither he could kill Flitwick, so both Sides would have asked some difficult questions. Therefore stupefying Flitwick is simply the easiest way of avoiding those circumstances.

I did not change the original answer, so that everybody can see how we managed to get to this conclusion. Also thanks to @DavidS for pointing this issue out.

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    While I agree with the spirit of this answer, I think assuming Snape knew he had to go kill Dumbledore is jumping the gun. More reasonable that he knew he had to investigate the Death Eaters, and to do this he had to be prepared to join them (since if they're bold enough to attack Hogwarts something major must be going down). If Flitwick had been following him when he meets other Death Eaters he'd be put in a very uncomfortable position - they might expect Snape to assist them in killing Flitwick, or anyone else who got in their way. – DavidS Jun 23 '15 at 9:41
  • @DavidS While I would clearly agree with the "Snape had no idea what was going on"-Part of your comment, I have to disagree with the rest of your comment. As far as I know, it is pretty clear that the Death Eaters have conquered the school. Much more I believe (but I'm not really sure about that), Snape knew about the plan of killing Dumbledore, as he knew about the task Voldemort gave to Malfoy. So I guess Snape was pretty sure about what was happening and what has to happen on top of the Astronomy Tower. Also the "Severus, please.." of Dumbledore states that it was well planned beforehand. – Zanser1609 Jun 23 '15 at 9:54
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    Snape definitely knew he had to kill Dumbledore, but at that moment he might not have even known Dumbledore was in the castle. WE don't even know that Dumbledore was - the Dark Mark was cast over the school before Harry and Dumbledore got back from the cave. And it wasn't a pre-arranged meeting - they went to the Astronomy Tower because a Death Eater cast the Dark Mark there, not because he planned to meet Snape there. Snape would be making a thousand unwarranted assumptions to hear Flitwicks remark and IMMEDIATELY decide he must kill Dumbledore. – DavidS Jun 23 '15 at 11:15
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    I edited my answer to fit the Information we gained in the comments. – Zanser1609 Jun 23 '15 at 11:33
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    Cool, I think that neatly answers the question :) – DavidS Jun 23 '15 at 11:41
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Just to keep all the possibilities covered, I'll be a devil's advocate.

It is possible that Flitwick had collapsed and Hermione jumped to conclusion afterwards to fit her theory.

It's unlikely, but possible. Otherwise @Zanser's answer is correct. +1

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Not to mention, of course, that while Filius Flitwick might have been caught off guard by Snape's attack because he did not expect a colleague to try and stun him, if Flitwick and Snape entered the heat of battle and the Charms Master had mentally readied himself to fight, if Snape gave any sign of having gone rogue, Flitwick IS a former Dueling Champion, so if he raises his wand to incapacitate Snape, his chances of succeeding is significantly greater than Harry's when he pursued Snape following the murder of Dumbledore. If Flitwick did manage to defeat Snape, with whom I believe him to be on par if not having a slight edge due to experience and presumably a slightly more versatility in martial magic, Snape would be left unable to meet the condition of the unbreakable vow and die, leaving Draco to potentially face the wrath of the Dark Lord when or if he failed.

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