Board Thread:Questions and Answers/@comment-31293457-20170212215226/@comment-31333672-20170221013243

Actually, they never leave the underground in the boss battle. This is explained by the pacifist run, Frisk and myself duel one another, until I reliquish from fighting, and then destroy the barrier. Frisk and Flowey were probably dueling in the barrier space, but flowey was too fat that the player could not see the light, or flowey transported both Frisk and himself to another area. Maybe a space that only time-line controllers could be in, which is why Frisk and Flowey are present, and someone like Sans is not shown disrupting the fight to save the timeline.