Chasing Shadows is probably the single most difficult mission in ST:R due to a combination of luck and how wingman AI handles enemy targets. You have plenty of wingmen in the mission, but you also have a wealth of hostiles--I think you can end up with 20 or 30 kills if you fly aggressively--and your wingmen get so bogged down in attacking fighters and enemy transports that they forget to prioritize the defense of the Hope. The Medusa bombers are by far the biggest threat to the survival of the Hope, but if they jump in while your wingmen are busy with other targets, they won't break off to attack the bombers unless you order them to. This often results in a situation where you have to fly bomber defense single-handedly, which can't be done realistically because there are too many bombers and each Medusa can take a lot of punishment.
The way you've completed the mission is effectively a cheat that exploits how the scripting works in order to give you fewer targets to engage. Not pointing any fingers, but the mission can be completed "normally," and in a way that allows you to complete all of your objectives. If you should decide to rerun the mission through the tech room, here are some tips that might make things run a little more smoothly:
- Don't use your leech cannon, as it consumes too much energy and inflicts no damage. Limit yourself to the Prometheus.
- Rearm yourself frequently, at least until the Medusas begin jumping in. Missiles will help you make short work of the Zeus bombers and Valkyries. (You can ignore the Lokis, for the most part, as your wingmen will usually be able to handle them.)
- When the mission begins, order your wingmen to engage all targets.
- Immediately go after the Zeus bombers making a run against the Hope. Once they're dealt with, immediately start scanning the Vasudan cruisers; don't wait for orders to do so. Let your wingmen handle the Leviathan cruiser.
- The first Zeus attack wings should begin arriving shortly after you finish scanning the third transport. Shoot them down quickly and rearm if you need to.
- When the enemy transports and freighters start jumping in, go after the Valkyries first so they won't harass your wingmen. You can target the transports and freighters afterward. Don't spare your missiles, as you can still rearm at this point.
- It's in your best interests to protect the Vasudan cruisers, as they will continue firing upon enemy targets even once they have been evacuated, but their survival is not required; your secondary objective is tied to the medical transports, not the cruisers, and once they've jumped out, you can let Zeus bombers destroy the cruisers if they're taking up too much of your time.
- Once the Medusa bombers begin jumping in, order all of your remaining wingmen to defend the Hope. Prioritize destroying these bombers at all times; you will no longer be able to rearm yourself because the bomber wings will jump in too quickly for you to replenish your missiles.
- Once your wingmen are ordered to defend the Hope, they will continue to engage enemy ships that they deem a threat to it, including the freighters and transports. If there are other enemy targets on the field when the Medusas arrive, it may be necessary for you to manually order your wingmen to attack them. This can potentially cost you the blockade objective, but as you've discovered, the bombers will simply destroy the Hope if they aren't cut down quickly.
- Continue to run bomber defense until the Hope jumps out.
- You can jump out as soon as the Orion arrives, or you can stick around a little longer to hear some extra snippets of dialogue and help the destroyer's fighter escort take out the Lokis that jump in. After you've destroyed several wings, you'll receive an order to return to base.