Three questions

[knowles2]

Telford arriving in the middle of the battle and saying: "follow me". How did he knew, that they control the ship?

They were of course, he linked up with destiny computers via the seed vessel.

He were track them on long range sensors for days, saw a sudden shift in course an presume the crew change course as he knew where destiny was heading was a recent war zone he thought destiny would avoid at all cost if the AI was still in control.

Just because there are not explanations on the show does not mean there are not simple solutions. Plus I am sure this series being serial mean the events that took place on the seed vessel will be revealed over the course of the rest of the season, they had more important things to be getting on with such as escaping drones.

[knowles2]

So they used rush as a template to work off of to modify chloe..

No they just relies Chloe was to thick to relies what there plans would be, why Rush already able to turn there computer devices against them, was to smart for there programming to work on him. If they did do it to Rush he probably would of just taken control of the programme they implanted in his head an turn it against them.

The thicker you are the more likely the reprogramming would work.

An they went after the thickest person on the ship.

[Open The Iris]

there is an even bigger question i can think of unless im going daft. by how come telford is still around. he is meant to be in someone elses body for a start. then he was abandoned in the seed ship. did no one think to disconnect the poor hapless volunteer connected to the stones. thus putting telford back in his body on earth. skip on a few episodes to when Ginn is killed, and we can clearly see she is the only one connected to the stones

that is one big plot hole

[Artemis-Neith]

there is an even bigger question i can think of unless im going daft. by how come telford is still around. he is meant to be in someone elses body for a start. then he was abandoned in the seed ship. did no one think to disconnect the poor hapless volunteer connected to the stones. thus putting telford back in his body on earth. skip on a few episodes to when Ginn is killed, and we can clearly see she is the only one connected to the stones

that is one big plot hole

For a start, Telford's body came together with the LA people onboard Destiny in season 1, "Incursion, part I" (ep. 1.19). In the moment he arrived on Destiny his consciousness changed with Rush's, and both men were back in their own bodies, Rush in the infirmary, and Telford in the Gateroom with the LA people.

Then in season 2 he was left on the seed ship in "Awakening" (ep. 2.3), and explained after his coming back in "Resurgence" (ep. 2.10) that the aliens who were on that seed ship kept him alive, and that's the reason, he could come back with the same seed ship, and the same aliens still on that ship in that episode.

Everything was explained, your plot holes are just your own lack of information. Of course you have to watch the episodes, one after the other, otherwise you'll not be able to understand the storyline. That's for sure a problem with this kind of serialized series, if you miss one, or more episodes, you're lost, and it's impossible to understand anything. If you're not willing to invest the time to watch all episodes, you should really go on, and find something else to watch. Because this series will never be your cup of tea.

[Open The Iris]

yup my bad i did forget about that bit