Following the events of The Valley of the Pagans, the band arrives on Plastic Beach and are lying exhausted on the shore. Murdoc takes off a Boogieman gas mask, and we see that Russel has returned to his gigantic size. Noodle comes out from inside of Russel's mouth before he reverts to his normal size. 2-D vomits up a whale and we see The Pink Phantom fly off into the sky. The band sees multiple memorabilia from their time at Plastic Beach, including Daley's skeleton on the shore, the crashed planes and ships of the Black Clouds, Noodle's broken Oni mask, and Cyborg Noodle inside of a submarine. Just as the band was overwhelmed with memories of the island, a giant sea monster (Leee John) rises up from the ocean floor wrapped in chains and begins to destroy the island with his laser eyes. The band heads to the lighthouse to take cover as the monster slices the island, sending the submarine with Cyborg Noodle inside sinking to the bottom of the ocean. The monster then uses his laser eyes again on the main building and destroys it, leaving it a smoldering ruin. The monster then returns back to the depth of the ocean, leaving the band floating on a lighthouse island. As the lighthouse slowly sinks, a portal opens and Russel, Noodle, & 2-D escape to safety. However, Murdoc doesn't make it and the portal closes, seemingly leaving him behind. But the portal reopens and 2-D grabs Murdoc and brings him though at the last minute.
This is also the second time that Plastic Beach was attacked (the first being in the Rhinestone Eyes storyboard).
The events of The Valley of the Pagans and The Lost Chord in a way ended Phase 6 parallel to how Phase 3 began with Stylo and On Melancholy Hill ; the band driving the car into the ocean and arriving at Plastic Beach.