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I wonder how long the MIB were stalking his family though.

Spoliers for Distant Memory and Souviner(episode 90) below. Read at your own risk!:

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Aelita's mother was abducted by the MIB shortly after making that large snowball-shortly after she agve Mr. Puck to Aelita fro Christmas. Also, the Lyoko gang later learns that Franz Hopper was an alias to prtect Aelita from the MIB. His real name is Waldo Schaffer- which explains the name on the folder during the end credits, and Hopper was Mama's madien name; Anita Hopper!
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The episode: I could guess from the music they played when he showed up what was gonna happen. You can always tell what the writers are trying to say by whether they change the background music. Slight drum roll is not gonna cut it.

The character: I've seen my share of fascinating theories on him. Of course, I helped that one guy and I don't know if it's gonna make it in his fanfic or not... anyway, here's my three main thoughts on him:

1. He was one of the lamest guys at Project Carthage, but he picked up the skills faster than he usually picks stuff up. (Yeah, I also think he was kind of slow. 2,546 is a big number.)

2. His best teacher was his wife. Antea Hopper. After what happened, the poor guy had to stumble through the Lyoko project on his own, and look how XANA turned out without her help! The scanners were a success though, I'll give him that.

3. I would NOT want him as my middle school science teacher. I mean, sure, my teacher was an enormous man who had once been in the military, but think about it. "Now, for the next class project, I want you all to write a program that grants the key to Lyoko to the first two DNA signals it detects. You'll get your grades back on June 1st."

(I should really start writing that story instead of just giving away plot secrets. ><)