For those of you who have no idea what I'm talking about, The Sulaco is an EEV ship that Ellen Ripley crashes in on a double Y chromosome prison planet - the film I'm talking about is Alien, more specifically between Alien 2 & Alien 3.
We'll start with a small background, In thes e first Alien, the Nostromo hones in on a distress beacon coming from LV-426, the ship was on it's maiden voyage home when the crew are awoken from hypersleep to see that mother has altered their course.
It's decided that they would go and investigate the planet, they find a derelict spacecraft (looks like a giant dog shit) and 3 members go inside, Kane, notes some strange eggs with organic lifeform in them, in the next seen, you see the "face hugger" jump and attach it'self to him, he then gets back to the Nostromo and into the infirmary.
They try and get the face hugger off, but they are unable to do so, discovering that it has pure acid for blood and it would kill him in taking it off, they note that it has some kind of tube down his throat and come to the conclusion that it's keeping him alive somehow - some time passes and then you see that the facehugger detaches itself because he wakes up, Ripley finds it on the ceiling of the infirmary. In the next scene, you see that they're all around a table and the alien finally hatches out of his chest (see below).

..and so the hunt begins, the android on board, Ash, has been communicating with mother and they want him to bring a sample back, all crew are expendable, to cut a long and epic story short, the Alien is jettisoned by Ripley and RIpley goes to sleep and way off of course.

In Alien 2, she is picked up by the company 58 years (off of the top of my head) later and is grilled by the company as to why she self destructed a company ship costing them millions of $$$. Skipping ahead, they lose contact with LV-426 which was the original planet from Alien 1, this has now been inhabited with teraformers (also known as engineers), their job is to make the planet habitable for others by doing something with the atmosphere. Ripley is asked to go back to the planet in which she reluctantly agrees to.
Her, along with this company berk, Burke and a commando team find no signs of the teraformers about from a little girl (who you see a short scene at the beginning of as her dad is caught by a face hugger - they discover the dog shit ship), the little girl explains to her what happened and when they visit the infirmary, they see 3 face huggers in plastic tubes. Long story short, they discover the colonists by the cooling tower with faint life signs, so being the nosey people they are, they go along to discover its a dirty trap!

The majority of them die as the aliens swoop in and try and kill them all, a selected few escape and call in the escape craft to get back to the mothership, which funnily enough has an Alien aboard that crashes it is where the famous 'Game over man, game over' line comes from.
Skipping vastly ahead to the final few scenes, Ripley runs after Newt as an Alien tries to grab her and discovers the Alien queen connected up to a large egg sac, she destroys the egg sac and runs back to the ship where Bishop, the android flies her away to the mothership, the Alien Queen somehow manages to get aboard and slashes Bishop in 2, after a funny fight (how she doesn't die I dunno), but she too gets jettisoned into space, remember that point. Ripley then goes into stasis with Newt and Bishop is bagged as he's in 2 halves and the other survivor is injured and put into a pod.
THE CONSPIRACY?
This is where it gets interesting now, at the start of Alien 3, you see small little clips of a face hugger inside the EEV attaching itself to a female face, later its discovered that Ripley has an Alien Queen embryo inside her and that she was the one who got face hugged, but let's look at the facts that the film gives us and how they imply what was seen.
Ripley is impregnated in deep space before the escape vehicle was jettisoned to Fiorina 161 (the prison). You can see the facehugger attached to her in the computer scan of her pod below.

The pod she is in is not infact, before the escape vehicle is jettisoned, there is a hole.

So that's it right? That's how she got infected? Well that's what the film showed us, but there are many more different ideas behind it. We'll take a step back and start from the beginning.
There was clearly a facehugger present from the above shots, but who was the host? Newts cryo tube glass plate is cracked by the facehugger injuring it causing acid to spill on the floor, this causes the electrical fire.

You next see the facehugger on a scan attached to someones face, from this alone and the previous scene, I feel that Newt is indeed the victim. However, a few more shots later, Ripley's face is seen, with no face hugger and she appears to be having some sort of a seizure, she's in her tube, but after the inter cut of a bolt exploding, there is another shot of Ripley with her glass plate cracked open.

Mystery solved? No.
That suggests that Ripley is the victim, we know this from the film, however, both Ripley and Newt's cryo tubes slide out into the EEV and none of them have a face hugger attached to them.

The only evidence we have is that Ripley hatches an Alien towards the end of the film, but there is no clear cut evidence that she was indeed the Facehugger's target.

At the beginning of the film, we see a bio scan shot of the facehugger on one of them, this is true, 100% correct. The warning message says that 'Stasis interrupted, fire in cryogenic compartment, repeat, fire in cyrogenic compartment, all personnel report to emergency escape vehicle launch of deep space lifeboat will commence in t-minus 20 seconds.', we can therefore deduce that the cryo tubes are to be loaded into the EEV, after the warning, you see Ripley with NO facehugger, so that indicates that the impregnation time was incredibly short (considering the first film when it took several hours), so surely one of them should have visible evidence of a face hugger.
At the crash, we see Newt's cryo tube, the crack on the plate is incredibly narrow, this suggests to me that it's too short for a facehugger to get at her.

There is other evidence off screen that suggests to me that is indeed Newt who was impregnated - this is from the December 1990 draft.
There was an Alien 3 comic released nearer the time and this I can see as being quite plausible, it's determined that Newt has infact drowned, this is again, from the draft.
In the comic, there is a picture of an Alien queen coming out of her mouth and then going into Ripley.
So mission accomplished, when you watch the first few scenes, it's hard not to get confused, wrong. 2 hosts, what?
The biggest issue I have with the above, is the Facehugger one. We know and see from the film that a regular facehugger is on board, there is ONE egg, but Ripley is impregnated and so is the Dog(who hatches a fully grown xenomorph like wtf), most people seem to think it's a super facehugger with amazing impregnating powers. However, some of this seems believable because this particular facehugger is relatively larger than normal, it has webbed like fingers and a skeletal structure resembling the queen, this facehugger is supposedly able to lay 2 embryos, one being a queen and the second a normal embryo, this facehugger is not seen in the theatrical cut of the film, but there is a short glimpse in the assembly cut, this gets more confusing because it then suggests that there were infact two facehuggers on board the Sulaco and EEV.

What makes matters worse is in the normal version of the film, after the EEV crash, we see the dog barking inside the wrecked EEV at the facehugger, this is a standard facehugger, not one of the elite awesome ones. But wait, we know that a facehugger can only infect one person, so was this the one that got Newt? Ripley? Why is it not dead? Were there two face huggers? We definitely know that it attacks Spike the dog, from evidence around the dogs mouth and the fact that we see the Xenomorph hatch from the dog - so eople now think that there were two facehuggers on the EEV/ship, but where was the second egg?

Alternatively, you just have to convince yourself that this facehugger can lay two embryo's to solve it, late ron in the film, Ripley awakens Bishop, the android and quizzes him about the fire on board, when Ripley asks Bishop, "Was there 'AN' Alien on board," Bishop says yes, AN, to me, meaning singular. So what gives?
So the question I ask to you, is how do you think/know how Ripley was infected with the Embryo?