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You should begin with the ships you built in the previous mission. A couple of the tranports will be under attack right away so use your interceptors to help them. You need four transports to complete the mission. If you get all six you'll get two elite units, one gunship and one bomber. These are fairly useful in the early missions so you should strive to save all the transports but don't worry about it if you can't.
You will be advised to build more resource collectors to harvest resources faster. Naturally, you will want to do so. I recommend you build two more to bring your fleet to a total of three. Since two of the transports come under attack right away you should send your interceptors to eliminate the enemies attacking them one by one. If you have four bomber squadrons as I recommended you can have them start attacking the Vagyr carrier right away. Its destruction early on would greatly aid your cause and make the mission much easier. Begin by having the bombers focus on the fighter facility, which is at the top of the carrier near the middle. When it's destroyed the carrier will cease production of fighters. Retreat your bombers to the mothership when it's destroyed so they can heal up (dock them with the d key). They can return after they heal to continue to pound the carrier.
Keep your interceptors on the move defending the transports. If a squadron gets damaged send it back for repairs at the mothership by using the 'd' hotkey while it is selected. It's important to remember while your mothership is producing resource collectors to get the new ones harvesting minerals as soon as they are produced. Your income will triple by the end of this mission; getting that second one going right away doubles it immediately.
Keep defending the transports - it'll be easier as they keep coming in, and you'll soon be able to build a corvette facility. Gunships would be useful to you here but they're not that great as the interceptors are faster and can more quickly move between the transports. I recommend building a couple more interceptor squadrons to help your existing ones deal with the enemy fighters. If needed, split your interceptors into two groups to deal with the enemies. Kill the assault craft before the bombers as they can fight back on your interceptors and it won't do you any good to lose them this early.
The Vagyr will eventually attack with frigates so your bombers will come in handy at eliminating them. A friendly ship will also jump in to give you a hand. At this point the mission becomes much easier. Your final task will be to destroy the Vagyr carrier once and for all. It should be at least somewhat damaged from your bomber runs. You can research increased fighter and bomber speed during this mission and I recommend you do so. The friendly Ferin Sha fleet will be more than happy to finish the carrier off for you, just give them a hand.