These are clue events you should see in Ch. 3 (all but one take place at Mi'ihen):
POINT 01 - YOU MUST ABSOLUTELY-VITALLY-IMPORTANTLY VISIT MI'IHEN DURING
CHAPTER 3!!! IF YOU DON'T, SAY SAYONARA TO YOUR MASCOT AND ATTEMPTING TO SOLVE THE MYSTERY.
POINT 02 - Machina Mayhem mission is where all is at. First important
decision is to start the mission by entering Mi'ihen either from
Luca or from airship. DO NOT ATTEMPT TO START THE MISSION BY
ENTERING MI'IHEN FROM MUSHROOM. If you do it anyway, you'll see
Prophet run off in direction of Mushroom Rock (this adds some more
points toward him.
POINT 03 - While you're dismantling stuff, forget about treasure chests for
now - you can always storm them later. Follow these step-by-step
guide:
-> three fights on 'Highroad - S end'
-> one fight on 'Highroad - S'
-> three fights on 'Highroad - central'
-> nothing is happening on 'Highroad - agency, front'
-> three fights on 'Highroad - newroad, N'; here's how it goes -
you'll come to a U-turn with a small elevation being 'caught'
in its center; atop this elevation is on of rogue machinas
threatening a woman which can be seen kneeling down; if you
already have 7 machina sets destroyed, skip this machina and
continue on (otherwise fight it by holding Circle and jumping
there); when C-turn ends, path will be turning left and on
mini-map you will see two more green squares, denoting two more
machina sets - one can be fought just before you leave Newroad,
and the other is positioned on an elevated ledge TO THE RIGHT
OF YOUR POSITION, and it seems like there's no way for you to
reach it; well, you can - hold Circle and walk near the edge of
Newroad; Rikku will jump down first, followed by Yuna and Paine
- in the end you will engage in combat with the machina on that
elevated ledge I mentioned; you MUST ATTACK this machina the
way I described it as it is vastly important for final touches
on Rikku
When done, you will end up with 8-10 dismantled groups. You win!
Carefully look at the crowd of people you'll see in the end. DO
NOT PRESS X UNTIL YOU SEE RIN! He'll be at the rightmost end of
the screen! If you're unsure, wait until he's in camera angle for
second time.
POINT 04 - After mission is finished, MAKE SURE YOU VISIT 'HIGHROAD -
NEWROAD, NORTH'! You will see Shinra who will tell you about
dropped CommSphere. This is the final nail in Rin's coffin.
POINT 05 - Make sure you don't miss talking to Prophet and his assistant
(both can be found on 'Higroad - north end'.
POINT 06 - Likewise, talk to every available Al Bhed person on Mi'ihen.
POINT 07 - In Luca, attempt Sphere Break tournament and win against Shinra in
the finals (a subquest involving Rin!).
You now have four definite suspects: Prophet, Chocobo Eater, Rin, and either
Calli or Rikku. Of course, in Rin's case, you must still view the CommSpheres
in exact sequence to ensure he'll be the one responsible.