Once the Lone Wanderer approaches the ship for inspection, (s)he is immediately abducted by the mothershipZeta. Shortly after the kidnapping, Theta is presumably beamed up for repairs by Zeta and stored in the vessel's hangar bays.
↑Fallout 3 Official Game Guide Game of the Year Edition p.718: MZ1 Crashed Anomaly "Almost directly north of the MDPL-13 Power Station (as you follow the line of power towers) you pick up an odd radio signal: You hear mainly static and then some eerie garbled speech you can't decipher. Locate the remains of a house; something has crashed straight through it, digging a furrow into the hillside. This is Recon Craft Theta, an Alien scout ship! Round the front of the craft to uncover a strange body, thrown from the cockpit. When Mothership Zeta arrives (which you are unaware of), as soon as you step close to the cockpit, you are grabbed by a tractor beam, and sucked up into an Alien spacecraft to begin Add-on Quest: Not of This World." MZ1 Alien Homing Beacon "Once Add-on Quest: This Galaxy Ain't Big Enough... is completed and you return to the Capital Wasteland, Recon Craft Theta is gone (it's actually in the Hangar aboard the Mothership), and has been replaced by a Homing Beacon. Activate this Beacon if you wish to return to the Mothership for Elliott's aid, or you want to gather additional supplies from the chambers still accessible. You can come and go as you please."