Starting out with the end of Triage, we see Bulkhead lying on the ground still smoking. And let's not forget that Raf immediately told Fowler that Bulkhead was coming back. There's a reason for this - remember in Tunnel Vision when Miko called Fowler? He was telling Bulkhead to "drop the rock and come back home." At some point in Bulk's mission, Fowler wakes up and becomes emotionally invested, which probably explains why he so eagerly turns to watch Bulkhead's return.
I'm seriously hoping the first thing Ratchet does in this episode is tell Raf to send the groundbridge for Wheeljack. We know that the two of them bonded in the last episode, and it seems only right to call Bulkhead's partner for what may very well be his final hour (it was stated that the repercussions from this episode would affect the rest of the season; and let's not forget the writers had initially wanted to include Cliffjumper in the entire first season and then kill him off in the finale - they're not scared to kill an established character). Wheeljack wouldn't have even stayed on Earth if it weren't for Bulkhead's prodding, and I feel as though the only reason Wheeljack would stay if Bulkhead died, is if Bulkhead made that his dying wish (which would be cheesy, but whatever).
Additionally, when Soundwave returns to the Nemesis, Megatron says that he is confident that Knockout and himself would be able to retrieve the last two relics. However, in the preview for Toxicity, Megatron sends Hardshell instead. Megatron shouldn't be fearful of failing his troops, so something else has to pop up that would cause Megatron to send the Insecticon in his place. I'm pinning my hopes on that something being either Starscream, or the return of Breakdown's body with M.E.C.H. - or maybe Megatron just wanted to make sure Soundwave was all right, I suppose.
Next, looking at the timeline for these episodes:
At around the same time, Knockout, Bumblebee, and Arcee all leave for New York. After this, Bulkhead leaves for his mission in Toxicity, and is shortly followed by Optimus who leaves for the arctic. Simultaneous to Optimus, Starscream and Dreadwing embark on their arctic explorations. Ratchet and Wheeljack have the Jackhammer up and running at about the same time as Soundwave, and the three of them reach the skies leading to the relic at about the same time.
Ratchet and Wheeljack left at midmorning, and did not return to base until well after sunset, and although they were the last group to get going, were the first to return. Because Dreadwing possessed the ability to fly, his mission in the arctic was swift enough for him to reach the Nemesis before Soundwave's return. Soundwave arrived just after Dreadwing's debriefing, and Knockout returned to the Nemesis soon after. The Decepticons had a lot of blank space in this area of time - Megatron took Knockout and Soundwave to the medical bay (possibly sending Hardshell to retrieve the fourth relic on the way), and saw to it that Soundwave was back to work with the Iacon database before Bulkhead ever returned to base. It's obvious that Arcee, Bumblebee, and Optimus's missions are finished by this point - as the Decepticons they were up against had already returned, but they have not yet headed back to base for reasons I can't figure out yet.
Either the timeline is all messed up for these episodes, or something happens that makes all the bots too busy to return to base.