Athena's been working a long scheme since pretty much the start of Incredible Hercules; herein I've gathered all the relevant evidence to speculate about what it is.
About twenty images, so not for dial-up.
She first shows up in issue #113, when Herc puts in a call to her after he and Cho go on the run from the law; Herc just wants to get away, Cho wants to destroy SHIELD.
Point 1: she's already familiar with Cho, and wants Herc to take him with him.
He eventually comes around and decides to take Cho with him as a permanent sidekick. They join Athena in Vermont, where she immediately tells them that the world's threatened again. They go on the road.
She tells him about a past event where the Hulk (one of the more childlike versions) ended up on Olympus, and accidentally helped the Titans escape because he made friends with two crippled ones left at the entrance. Herc leads the charge to slay Cronus and co.
They sort out the business with the God-eater, and Herc offers his bloody had to the Hulk, who is repelled and flees.
Point 2: This is something that comes up a lot in this series: dickishness is next to godliness.
Anyway, they end up in San Francisco, and have a brief skirmish with the Eternals.
Ah, icon source; how I love you.
Athena's called together all the Skyfathers to deal with a certain planetary threat:
This is the start of a tie-in to Secret Invasion, which picked up on a very obvious tie-in possibility; since the Skrulls are waging a religious war, the gods of Earth realize it's deicide-or-be-deicide-ed. Athena convenes this meeting to put together a force to go kill the Skrull Gods. The other Pantheons (organized into continental blocs) agree, though they hit a bit of a snag because of the nature of the messenger:
The army of the gods turns out to amount to only a handful of people:
So they're off.
Point 3: Thor is pointedly kept out here. Of course, the meta-reason is that he had his own tie-in, but within the comic, this is Athena pushing Hercules for leader. This also led, for a time, to people speculating that Athena was actually Loki in disguise (while at the same time the comic played an is-she/ish-she not-a-Skrull game).
Anyway, the heroes win, and kill the Skrull god Kly'bn; his consort, Sl'gr't, seemingly survives, after killing the Japanese God of Evil Amatsu-Mikaboshi (the god who led the invasion of Olympus that killed Zeus):
Anansi called that one.
As with most of her plans, there's a short-term, surface objective, which Herc and Cho are aware of, and other ones that they're usually not:
Primary objective: Kill the Skrull Gods.
Secondary objective: Piss off Hera, precipitating a leadership clash.
Third objective (as I see it): Put Hercules into a leadership position.
Unintended (but beneficial) result: Mikaboshi ends up in control of an army of slave-deities; suggests she'll have a use for a unifying threat at some point in the near future.
She doesn't do a whole lot in the next arc; in #126, we get Herc's origin, which has a lot of stuff relating to her. First, in the opening, young Herc and some thugs talk about all the stories going around about Herc's origins:
So we learn that giving him all these superpowers and such was hers and Zeus' idea.
On a semi-related bit, the writers also choose to emphasize her role in the story of Tiresias:
That's normally the lesser-known of Tiresias the seer's two origin stories (he needs a Crisis-style continuity reconciliation).
Anyway, at issue's end, Herc's on his way up the hero ladder:
So she can apparently see the future too (you understand why the writers usually keep her behind the scenes rather than in combat).
Looking back to her first appearance, she's clearly known about Cho for a good long while.
Herc goes on to play a critical role in defeating a rising of giants against Olympus, and, according to the "Saga" included in #126, he fulfilled Athena's plan by killing all the monsters around Athens, thus facilitating their golden age.
In the next arc, Hera comes calling, and she's pretty pissed off.
Hera whines that all the other Skyfathers are laughing at her and saying she's a terrible leader (and also that she has cooties).
Later, Athena cops to deliberately trying to provoke this:
Finally, in the most recent issue (which I already posted), Herc and Cho head off to Hades to retrieve Zeus as a counter to Hera (which I don't believe is what she actually wants them to do). Zeus revisits the whole "gods need to be bastards" theme again:
Zeus says it was a mistake to create him.
Also on this trip, Amadeus visits with mom and dad in Elysium, which wasn't something he planned, but I imagine it's a part of hers, given her relentless focus on his development.
Now, there's a lot of theorizing that Athena wants the Skyfathership (or mothership) for herself, but I believe she's trying to put Hercules in that position. There's the aforementioned leadership role in the "Sacred Invasion" story, and Zeus' lines in that last panel above, which he rants that Hercules will never succeed him (something Athena disagrees with, at least to Zeus' face). Also, it almost certainly involves Cho having to do something he thinks is morally wrong, based on all the talk.