although they had known each other for only two years, he had indisputably become petter branson's

尽管他们才刚刚认识两天，但是他已经毫无争论的成为了petter brandon（人名）的不可缺少的副职官员。
他成为那个人的副职是在过去，所以用过去时，而他们两个认识是在成为副职前，所以前面用过去完成时。

因为although they had known each other for only two years中 for only two years，可用完成时态和过去时态（ He was in prison for 20 years)。

he had indisputably become petter branson's indispensable lieutenant

这句根据句意必须用完成时态。若这句用过去完成时，前面一句要用过去的过去的过去时态，但英语中没有这种时态，故只能用过去完成时。

句子可以改成：although they knew each other for only two years, he has become petter branson's indisputably lieutenant

因为他们是以前认识的，说的是以前的事情。所以就不能用现在式了
而后面一句是说他变成了petter的上尉
用过去是也是因为它是之前发生的。
而他现在已经是了。