She merely set off the bomb that blew him up.
You have to watch Dual realizing that everything that is said, is from the perspective of a in universe, person, human, on the ground, with no access to the knowledge or vocabulary as it applies to the overall Tenchi-verse. Dee and Kumu are effectively the only ones that know anything accurately in the grand scheme of things.
Dual Universe "dimension" A is where we're introduced to Masaki Yotsuga at the construction site.
For ease of thought, we'll say the universe MY pitches the bonding plate away in, remains Universe A.
The universe that MY keeps the bonding plate, is Universe B.
Universe B is shown to be Kazuki and MitsukiS's reality until they are both teleported to Universe C via the basement experiment. Universe C is the world that Kazuki has had visions of for so long, that includes mech fights.
Universe D is either a very similar reality to B/C, or a combination world (as discussed before) which is where we see
Kumu arrive in a shipping box and Jinbu arrive after being found underwater.
supported by those larger than us. But we dream... of the day when we will eventually
blossom under the wide open sky.