There's some sequence breaking going on in Last Hope, mostly because Isis Repair follows some weird pathfinding/docking logic. Two separate chains of events run parallel to each other: the arrival of Shivans and the repairs that Isis conducts on the Hope. The arrival of reinforcements (and the end of the mission) is triggered by the destruction of all Shivan forces and has nothing to do with the Hope's repairs, which are just window dressing for the mission. However, there's some in-mission dialogue that's tied to the progress of the repairs (triggered by the destruction of the three Dragons that jump in after you take out the Thunder).
The problem here is that repairs won't actually begin until Isis Repair docks with the Hope, which it seems in no hurry to do. Isis Repair jumps in around 6:25-6:30 and shows an arrival time of around 90 seconds, meaning that theoretically, it shouldn't dock any later than 8 minutes into the mission. However, Isis Repair doesn't travel to the Hope in a straight line and appears to follow a meandering, often circuitous path, meaning that it sometimes doesn't actually dock until the 10-minute mark or later. The mission clock is ticking all this time, meaning you'll get messages about the progress of the Hope's repairs before Isis Repair ever docks with the ship. (I think the deployment of Dragons may have been intended to alleviate this by keeping the player occupied and giving Isis more time to dock, but Dragons are easier to take out in FSO than in retail.) On my last playthrough, Isis Repair traveled to a point about 5km from the Hope, turned around, and started coming back, meaning that it never docked for the entire duration of the mission.
None of this stops you from completing the mission because all you really have to do to progress is kill Shivans, but it isn't doing immersion any favors, either.