Basically, the whole thing's pretty open ended and there's a lot of "why"s missing from the bigger picture.
WARNING: MASSIVE SPOILERS
This is what we know:
-Waidwen WAS Eothas (or something approximating a very powerful avatar) and he tried to take the Dyrwood by force.
-Magran responded to his attempt to conquer Dyrwood with the Godhammer.
-Woedica has been carefully plotting... something... since her fall.
We can try to fill in the blanks using info from dialog:
-Magran is apparently pro-progress. She supports the use of animancy and is apparently allied with Galawain/Abydon against Woedica.
-She does not see Durance, and yet Durance is able to channel her power.
-Woedica's plot is extremely meticulous and varied, spanning all the lifetimes of Thaos and culminating in recent events (eg. the Hollowborn phenomenon).
-The gods seem more like superpowered sentient avatars of specific concepts/doctrines (from the comments of the delemgan sisters and your conversations with the gods themselves) and they are bound to those concepts/doctrines on a fundamental level. Woedica (being the goddess of established laws and hierarchies) actively works against radical change of the status quo everywhere, for example, even in the conservative Aedyr Empire (her agents interfere with politics there just on general principle, based on Aloth's dialog).
-According to Durance, bad things happen when they try to take interact with mortals on a fundamental level (eg. Eothas' possession, the creation of the Godhammer).
-They have made a pact which prevents them from interfering with mortal affairs directly.
-Although Waidwen/Eothas displayed plenty of other agenda, he was still the god of renewal/light. Because Eothas attacked the Dyrwood RIGHT BEFORE the start of Waidwen's Legacy then Durance quickly came to the realization (and this makes perfect sense) that Eothas probably discovered Woedica's plot and was ultimately just trying to prevent it.
Note that besides Berath, Eothas is the god most affected by Woedica's actions, especially his Gaun aspect. Unlike the passive Berath, however, Eothas was an active god who would regularly communicate with his faithful.
The Watcher's hypothesis
-Through a combination of gut-feeling, visions (the death of the 11 other individuals who helped create the godhammer) and proximity to both Durance/Magran, the Watcher hypothesizes that Magran was a willing accomplice of Woedica - at least as far as the destruction of Eothas was concerned (it could just be an alliance of convenience at that particular point).
Durance's speculation based on the above:
-Magran was working closely with Woedica and deserves to be punished just as severely for her actions (particularly the part where she tries to get him killed). Based on his proud/vulgar nature, it's understandable why he latches on to one of worst possible conclusions one can make.
-The other gods knew about the Leaden Key and its activities but they tolerated the group (whether they agreed with Woedica's methods or not).
-Woedica decides to use the Leaden Key in what is possibly the highlight of her plot - a kind of rite of ascension which would involve her consuming thousands of powerful souls to gain MASSIVE power (the Hollowborn phenomena is a side effect).
-Eothas discovers the plot but unlike the other deities, he decides to act directly (god of renewal, change was fundamental to his nature so what can you do) by possessing Waidwen.
-To punish Eothas for breaking the pact and abusing his power (despite his intentions), Magran works with Woedica (because of Woedica's nature and because Eothas was already working against her) to orchestrate the creation and use of the Godhammer. She probably knew that by working directly through the mortals tasked with creating the weapon, however, she was also dangerously close to breaking the pact herself - to help mitigate this, everyone associated with its creation/use had to die (probably through Woedica's intervention - the Leaden Key?).
-Obviously that didn't work. Durance survived (and keeps surviving, thanks to you) and the reason he can channel Magran's power (even though she can't even see him) is probably because he has a shard of the goddess' essence/being/whatever inside of him.
-The alliance between Magran and Woedica ended there.
-If Deadfire gets an expansion, Durance will probably be the big boss ala reverse Bhaalspawn and you have to kill him before he "eats" Magran and destroys the rest of the deities in his crusade against them heh.
Edited by scythesong, 29 April 2017 - 08:56 AM.