Mega Man Supermeta

supermeta by Seth Kleinerman, Ricky Liu, Aaron Dinkin, and the metapuzzle committee
Mega Man world stucture by Seth Kleinerman and Aaron Dinkin

The six robots and their weapons are as follows:

Bebop Man: BLUE SHIFT
Bio Man: DNA DESTROYER
Blackberry Man: TELEGRAPH SWITCH
Craps Man: ODDS FINDER
Minus Man: ALPHA DECAY
Stagecraft Man: WORD SWORD

Each weapon clues some kind of wordplay operation that can be carried out on exactly one of the names of the other robots in order to produce a new word. This gives rise to a cyclic order of the six robots: Bebop Man's weapon defeats Bio Man, Bio Man's weapon defeats Stagecraft Man, etc., as follows:

BLUE SHIFT: Shift all "colors" (ROYGBIV) one space in the direction of violet on the spectrum.
BIO → IVY

DNA DESTROYER: Remove all DNA bases (ACGT).
STAGECRAFT → SERF

WORD SWORD: Prefix S to the beginning of the word.
CRAPS → SCRAPS

ODDS FINDER: Extract only the letters in odd position in the word.
BLACKBERRY → BAKER

TELEGRAPH SWITCH: In Morse code, replace dots with dashes and vice versa.
MINUS --/../-./..-/... → ../--/.-/--./--- IMAGO

ALPHA DECAY: Reduce the atomic number of all chemical symbols by 2.
BeBOP → HeLiCAl

Take these six words (IVY SERF SCRAPS BAKER IMAGO HELICAL) and insert them in the given boxes. There are two five-letter words, but you can discriminate which word goes in which box by the cyclic order of the robots.

As indicated, add paired letters mod 26 (A=1) and put the result in the circles in the center to spell out WILY COYOTE, the supermeta solution for the Mega Man gameworld.