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Do you think it would be possible to ally Sisters and Mechanicus by claiming that the Sisters are part of a Missionarius Galaxia unit attached to an Explorator fleet?

It makes sense to have your missionaries with the explorers, but with the political divisions within the Imperium I am unsure.

It would make sense, as the Ecclisiarchy might be sending some high profile missionaries and want then well-protected

Technically, the only Sisters who undertake Missionary work are the Orders Sabine, who do it the old-fashioned way - live amongst the wild tribes for a few years corrupting their children until everyone Believes.

That said, Sisters and Mechanicum have teamed up plenty of times in the past, and if the Ecclesiarchy has a big enough stake in the Explorators' mission (say, there's a lost Shrine World in their path) it would make total sense to send some Sisters along to guard their envoy, or even as the envoy themselves.