I love kicking Hader's ass, he makes it easy to dislike him. Since you mentioned Viper I assume this is the MSF storyline (you get to kick Hader's butt elsewhere too, the circumstances differ slightly iirc). It's been a while though so you'll need to refresh my memory.

You said you took care of Viper, that means you're with Admiral Trump right? Can you clarify exactly what you mean by "launching the admiral"? (Try to be specific, both Trump and Hader are admirals, it can get a bit confusing

If I'm not mistaken, you have a few goals: prevent the missile ships from destroying their target, destroy the missile ships, destroy Hader, keep Trump alive. Your main target is the missile ships (the "sappers" Hader talks about) and Hader himself. You probably lost because those missile ships delivered their payload - you need to take them out first. Taking out Hader should also stop the fight iirc.

Since there's several Hader scenarios and I don't remember exactly the MSF one, I can only give you a general strategy. Camp the portal Hader's forces appear from. Destroy the missiles boats first and if possible go for Hader directly. Torpedo him. Once he's destroyed you're usually safe, just mop up the rest. Your mothership doesn't need to join the fight, actually usually there's a bunch of hostile ships elsewhere in the system and I send it there.

You'll need to be a bit more specific who is in the system and what exactly are the mission objectives (see your quest log). Which station you're heading to, who else besides your team is in the system, which portal Hader's forces appear from.