The Phantom Virus was an alteration of Bill's baseball game
This would go a long way in explaining the infamous Idiot Ball the villain held. In an effort to save time, he simply altered his baseball game's code. Unbeknownst to him, this made the Phantom Virus a baseball fan too, creating an inadvertent trail back to him that he couldn't correct by the time he learned this. Bill is related to Lex Luthor
The Scooby gang have had many adventures with DC characters(canon or otherwise), and this guy shares several traits with Lex when he was younger: they're both egotistical geniuses, have a grudge against a former friend for an irrational reason, and are redheads(At least Luthor was at first).When Bill compared the Virus' reaction to magnets to Kryptonite, he wasn't referring to a comic book. He decided to take a page out of uncle Lex's book and concoct his own scheme to destroy his rival. In fact, for all we know, the two could be close enough for Luthor to bail Bill out of jail. The gang better not visit Metropolis any time soon.