Each ONIOM subcalculation may have a different set of MOs. You may use the "formchk" utility to generate separate formatted checkpoint files (fchk), one for each subcalculation so one can examine the different sets of MOs independently. The formchk flag that you need to use with ONIOM is the following:
"-XY" with
"X" being L, M, H for "Low", "Medium", "High" levels and
"Y" being L, M, S for "Large", "Medium", "Small" size systems
Here is an example of the 6 possible different formatted checkpoint files that you can generate for your 3-layer ONIOM job:
a) High level (td=(nstates=12)/b3lyp/tzvp) calculation on Model system (High layer atoms plus link atoms):
After you have the formatted checkpoint file (fchk) with the desired set of MOs from the ONIOM job, just open the formatted checkpoint file in GaussView for visualization. According to your email, if you only want to look at the MOs that were used in the TD subcalculation, you only need to generate the FCHK file from a) above (High Level calculation on Model system)
By the way, for a 2-layer ONIOM job, you only have 3 different subcalculations: