The Whispering Way wants nothing less than the death (and undeath) of all living things on Golarion. In the shorter term, many members of the whispering way want eternal unlife and/or great power for themselves.

This presents a couple of potential motivations for agents of the Whispering Way:

They might seek to expand the Eye of Abendego, causing massive death and destruction in the Shackles, Rahadoum, and the Sodden Lands.

They might want to raise an army of powerful aquatic undead from beneath the storm for whatever other purposes, including the above.

Most esoterically, the Eye of Abendego appears to be linked in some way to the death of Aroden. ~~Before Aroden was a god~~ [edit: Aroden had already been a god for hundreds of years by this point], and before Tar-Baphon, the Whispering Tyrant, was a lich, they fought each other on the Isle of Terror in a trap Tar-Baphon had set for Aroden. Tar-Baphon lost the fight and was slain.

Tar-Baphon is neither the founder nor a particular object of worship for the Whispering Way, but he is easily their most powerful member, their overall leader (though the Whispering Way is fractious, so that doesn't mean much), and by far their most successful member in pushing their objectives.

All this is to say that the Whispering Way might have some particular interest in the dead god Aroden, and might try to harness the power of the Eye of Abendego to try to bring back Aroden as some form of undead god. Whether this is something they can realistically achieve is up to you, of course, but it doesn't need to be possible for some of them to get the bright idea to try it.

Of course, they could also simply try to absorb some of the power of the Eye for their own uses elsewhere.