I completed this mission - there were 6 aliens on the map: 1 on the ramp of the building on the ride side of the ship, 2 in the ship who popped out on right side of the ship to shoot at my team, 1 more who popped on the left side of the ship to ambush, and 2 more in the building nearest where you begin, to the front-left of the ship.
This was a very tense mission. I did not cut through the ship, no no no. I covered the ship while I cleared that first building on the right side of the ship. Leaving behind 2 agents to cover that side of the ship, I advanced the other 6 agents around the ship, carefully, slowly, nice and careful. At the back of the ship on the ship's left side, 1 alien tried popping out, but I had all the doors well-covered, and that alien was toast - never got off a shot. Waited to see whether any others would pop out, then left behind 1 stormtrooper agent to cover all the doors while the other 5 advanced: machine gunner, grenadier, assult rifleman, sniper, and medic.
Moved these five in very open formation, with the sniper constantly covering the door of the distant building, up to the HUM-VEE to take cover. Moved the sniper up, as she shot it out long-range with an alien in the building popping out and taking shots before ducking inside for cover. Snuck the grenadier up beside the ramp, crouched, crouch-walked him around, and dumped 3-round bursts of plasma grenades into the doorway, killing one. The other took the hint and fled inside.
I got the assault rifleman and a stormtrooper (SMG-armed) up stacked covering the building door, with the machine-gunner and grenadier (flechette rounds now) covering the door from a more open angle, taking cover by the ramp, with the medic still behind the Hummer for cover, but in proximity in case she was needed. Lobbed a grenade in to frag the door-area, but the last alien popped out to "do its thing", only to be quickly shot down by the team stacking near the door.
Long mission, took me over an hour, but I like to be VERY careful: every move must be meticulously planned. Lost no agents, and all good. That was a huge ship, and I decided to clear the buildings and keep the ship covered before storming the ship. I always do the ship last: I don't want any aliens who were hiding in buildings walking up behind me while I'm stacking the doors and taking out the team. Luckily, I didn't have to storm that awful, huge, and convoluted ship.
Now I'm not getting any more missions. Does the game continue after this? I got the "Thanks for playing UFO:AI" message, but I tried continuing and saw no more missions for a couple of months. I sure hope I can keep going, just to do ground missions - I don't need more research to keep me happy until the next release. Does anyone know?