When Toffee got blown up by the Whispering Spell, his spirit didn't exactly get trapped in the wand crystal, but rather it became connected to the sea of magic itself (the "hobo stew" as Glossaryck would call it). From that place he could influence both Star and Ludo's wands, since they're both some kind of cosmic magical conduit. Eventually he took control of/corrupted enough magic that magic itself started to become unstable, causing "the fritz," which became extreme after he drained the Magic High Commission, both stealing their power and preventing them from dealing with the fritz.
Star uses the Whispering Spell on Ludo's wand/hand to try to kill Toffee, believing he was possessing the wand crystal. It's not clear exactly what she expected to happen, but the same thing happens to her that happened to Toffee: the Whispering Spell obliterated her body and her spirit was pulled into the "sea of magic" which at this point is almost completely corrupted. Toffee now has Star's soul at his mercy, and uses her as a hostage to get Moon to finally hand over his damn finger. Reconnecting the finger to his hand somehow canceled the effects of the Darkest Spell, and Toffee is able to fully regenerate his body out of the corrupted magic.
Meanwhile, Star('s spirit) is lost in the dark sea of corrupted, inert magic. She desperate skims the surface of the "hobo stew," trying to reach the last few chunks of golden, uncorrupted magic floating in the "stew." She dives after the last chunk, diving down deep until she starts to drown. Then she finds/hallucinates (does it matter?) Glossaryck, who reminds her she needs to DIP DOWN as she sees the last pure chunk of magic in the deepest part of the (literal) stew. She dips.
Dipping down deeper than ever before, she surges with magic as she takes control of the sea of magic herself, burning away Toffee's corruption. With this massive well of magic at her command, she tears a hole back into reality and obliterates Toffee.