Fly ball, no tag up, ball out of bounds on appeal

[SactoBlue]

Situation:
Runner on 1st, no outs, batter hits fly ball to RF. Runner takes off on contact, no tag up. Ball caught, fielder throws to cutoff, cutoff throws to 2nd baseman nowhere near 2nd then yelling starts - "No tag, no tag." Runner is now around 2B. Second baseman throws to 1B and fielder misses ball and ball rolls into dugout. I signal dead ball and play stops. Runner then retreats back to first underdead ball period. Where do I put the runner? He was around 2b when throw took place heading for 3b.