Seriously, how did Jeff Goldblum get the virus from a Mac into the mothership's mainframe? When they docked, he didn't hook up any type of cables or anything like that, did the mothership have Wi-Fi or something? It is all very confusing to me...
Answer
For your actual question: The laptop was hooked up to the ship they flew in on. The ship in turn was connected wirelessly to the mothership (which is how the auto pilot was able to guide them in) and then subsequently connected directly to the ship when it docked. The laptop is clearly hooked to the ship because he uses his laptop to open the ship's outer hull / windows.
In this image you can clearly see the cables running out of the back of his laptop (bottom right corner).
Now for the follow up question - How was a MacBook able to communicate with an alien spacecraft? Here are a few things to consider:
- At the beginning of the movie the aliens were using our satelites to coordinate their attack, which suggests their technology is already compatible in some way.
- Jeff Goldblum was able to isolate the alien signal from the satelites, so he is becoming familiar with their technology
- The alien ship in Area-51 has been there for 50 years
- They've already learned some ways to interface with the ship
- Because we've been studying it for 50 years, some of our technology might secretly be a derived from the alien technology, making it more compatible
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