If we reject the OPs "jumping in" and assume the statement is from a person who's watched too much sci-fi, what would we see as the alien fleet arrives?
Well, the first question is, what methods do we know of right now that could work for the alien's engines?
There are :
1. Nuclear salt water or nuclear pulse (orion drive)
2. Fission Fragment
4. Black holes
5. Antimatter annihilation
6. Some kind of sci fi method to just release the rest mass as energy in ordinary matter without the antimatter needed.
Number 1 is some variant on a fission bomb propelling the ship. A couple percent of the speed of light, tops. Number 2 and 3 have the problem of pathetically low thrust although high isp. Black holes depends upon assumptions about a black hole that makes them movable (they have to be electrically chargeable) and constructible (you need solar system sized mass drivers to accelerate metal rods to slam into each other at a sliver below the speed of light to form the black hole). But, they are a near perfect form of engine - you feed the black hole a particle beam of ordinary matter, collected by ramscoop, and you get back gamma rays that your enormous ship reflects like a parabolic dish. Antimatter annihilation is similar to black holes except it requires you to carry all your antimatter with you, and it's immensely difficult to avoid blowing up the ship.
Anyways, all these methods have a common factor. All of them will release a flare of gamma rays as the alien fleet decelerates. The alien fleet probably would not even use their engines except to maintain speed and slow down - they'd probably use a stream of mass accelerated pellets launched by mass drivers in their starting system to reach their cruising speed.
Also, all these methods have the problem that they provide pathetically low acceleration. 0.1 g (1 m/s^2) at best, a tiny fraction of that at worst. Realistically, the alien fleet will be decelerating for about 10 years to centuries. We'd be able to see the gamma ray flare from this for many years if a gamma ray telescope is pointed the right way.
As for vulnerability - they'd be immensely vulnerable upon arrival. Not to the technology we have now, but technology we could probably develop relatively rapidly. The alien ships would not have high acceleration engines able to avoid incoming fire or outmaneuver attackers because that kind of engine is too inefficient for interstellar travel. Their ship is unlikely to have anything on it more than a payload of factories and data, because the mass for weapons or engines is too much.
Their plan would almost certainly have to involve decelerating to rest near an object with some mass in our solar system, preferably one close enough to the star so that solar energy is available. One of the various comets or asteroids would do fine. They'd eat the rocks, turning it into more equipment, and essentially regrowing all their technology and infrastructure from the actual starship seed payload.
This is when you jump them. You need an orion drive space battlewagon to show up before the aliens eat enough rocks to build something to fight with.