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You only gain Bugfrags while the SP is out. If some else has their SP out, and you do not, you do not gain any BugFrags.
You gain 1 Bugfrag/per 20 HP of the Viruses you destroy. This is per virus, and is rounded up. If multiple Navis are present, the one in control of the SP only gets BugFrags for viruses they actually delete. BugFrags are similarly split in this manner when multiple Navis have SP's.
-Do you gain bugfrags from deleting navis?
-What if you don't delete them and only cause them to EJO?
-What if they ran from battle rather than you causing their defeat?
-Regarding "the one in control of the SP only gets BugFrags for viruses they actually delete" part, does the number of bugfrags gained have to do with the amount of damage dealt or do the total rewards of the kill simply go to whoever dealt the finishing blow?