As explained under 3 Nephi 1:22, Oliver Cowdery frequently omitted the subordinate conjunction that after “it came to pass”, although usually only momentarily. Here in Ether 13:18, he supra- linearly inserted the that later, probably when he proofed 𝓟 against 𝓞 (which is not extant here); the level of ink flow for the correction is somewhat heavier. The inserted that is much like the supralinearly inserted all that occurs later on in this page of 𝓟 (see under Ether 13:20–21). Not only is the level of ink flow for both corrections the same, but the insert mark in both cases is smeared in the same direction. Moreover, the all in verse 20 is extant in 𝓞, which argues that here in verse 18 the subordinate that was in 𝓞 and not added in 𝓟 as a result of editing on Oliver’s part.
We should also note that here in Ether 13:18 the that that occurs after “in the first year” is a relative pronoun and not the subordinate conjunction that. Earlier, in Ether 13:13–14, the text mentions that Ether was hiding out in the cave, so in verse 18 the text specifies that this large number of deaths occurred during the first year of his hiding out in the cave.
Summary: Maintain in Ether 13:18 the that that Oliver Cowdery supralinearly inserted, apparently when he proofed 𝓟 against 𝓞; the that was probably inserted here because that was the reading in 𝓞.