Oh man, how did she know he was the Phantom? Or did she? If her brother was killed by the Phantom it's a safe bet that it was either an accident or he was a Wraith worshipper. Please update quickly.

Author's Response: Actually, she doesn't know John's the Phantom; she's just targeting a high-ranking member of the Atlantis expedition.

As for your comment about why the Phantom may have killed her brother... just think about what notable episode took place this season involving someone being captured by someone, and you may work out what's coming up next...